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1.1M PDF - Theoretical Biophysics Group

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1. 17 e The exit command writes output files and exits cleanly e The abort command concatenates its arguments into an error message and exits immedi ately without writing output files e The numPes numNodes and numPhysicalNodes commands allow performance tuning parameters to be set based on the parallel execution environment e The reinitvels command reinitializes velocities to a random distribution based on the given temperature e The rescalevels command rescales velocities by the given factor e The reloadCharges command reads new atomic charges from the given file which should contain one number for each atom separated by spaces and or line breaks e The consForceConfig command takes a list of 0 based atom indices and a list of forces which replace the existing set of constant forces constantForce must be on e The measure command allows user programmed calculations to be executed in order to facilitate automated methods For example to revert or change a parameter A number of measure commands are included in the NAMD binary the module has been designed to make it easy for users to add additional measure commands e The coorfile command allows NAMD to perform force and energy analysis on trajectory files coorfile open dcd filename opens the specified DCD file for reading coorfile read reads the next frame in the opened DCD file replacing NAM
2. Partition 1 contains those atoms whose interactions are switched up as increases i e flagged with 1 in the alchFile Partition 2 represents those atoms whose interactions are switched down as A increases i e flagged with 1 AA values for each component are obtained by integrating from A 0 to 1 using the respective ELEC VDW LAMBDA listed for each partition after the title Analysis is handled by the NAMD_ti script available from http www ks uiuc edu Research namd utilities Although the output format of NAMD_ti pl may appear to lend itself easily to interpretation of the individual contributions to the free energy total elec and vdW for each partition this is rarely appropriate as these values are path dependent For example an output such as 10 LA KASSSSSEE 3 ASS 0 0 0 2 lambda Figure 10 Sample TI data log Y against A The blue shaded area shows the integral with fine sampling close to the end point The red area shows the difference when A values are more sparse In this example insufficient sampling before A 20 1 can result in a large overestimation of the integral Beyond 20 2 sparser sampling is justified as dE dA is not changing quickly Part 1 0 5748 6 3452 6 9200 Part 2 0 5391 4 9387 5 4778 Mea aaa aaa ale Subtotall 0 6048 0 3293 Total deltaG for transition lambda 0 gt 1 12 3978 sense may encourage
3. e selectConstrZ lt Restrain Z components of coordinates gt Acceptable Values on or off Default Value off Description Restrain the Cartesian z components of the positions 5 6 3 Fixed atoms parameters Atoms may be held fixed during a simulation NAMD avoids calculating most interactions in which all affected atoms are fixed unless fixedAtomsForces is specified e fixedAtoms lt are there fixed atoms gt Acceptable Values on or off Default Value off Description Specifies whether or not fixed atoms are present e fixedAtomsForces lt are forces between fixed atoms calculated gt Acceptable Values on or off Default Value off Description Specifies whether or not forces between fixed atoms are calculated This option is required to turn fixed atoms off in the middle of a simulation These forces will affect the pressure calculation and you should leave this option off when using constant pressure if the coordinates of the fixed atoms have not been minimized The use of constant pressure with significant numbers of fixed atoms is not recommended 63 e fixedAtomsFile lt PDB file containing fixed atom parameters gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to use for the fixed atom flags for each atom If this parameter is not specified then the PDB file specified by coordinates is used e fixedAtomsCol lt column of PDB containing fixed atom parameters gt Acceptable Values
4. NAMD User s Guide Version CVS 2015 12 17 M Bhandarkar A Bhatele E Bohm R Brunner F Buelens C Chipot A Dalke S Dixit G Fiorin P Freddolino P Grayson J Gullingsrud A Gursoy D Hardy C Harrison J H nin W Humphrey D Hurwitz A Hynninen N Jain N Krawetz S Kumar D Kunzman J Lai C Lee R McGreevy C Mei M Nelson J Phillips B Radak O Sarood A Shinozaki D Tanner D Wells G Zheng F Zhu December 17 2015 Theoretical Biophysics Group University of Illinois and Beckman Institute 405 N Mathews Urbana IL 61801 Description The NAMD User s Guide describes how to run and use the various features of the molecular dynamics program NAMD This guide includes the capabilities of the program how to use these capabilities the necessary input files and formats and how to run the program both on uniprocessor machines and in parallel NAMD Version CVS 2015 12 17 Authors M Bhandarkar A Bhatele E Bohm R Brunner F Buelens C Chipot A Dalke S Dixit G Fiorin P Freddolino P Grayson J Gullingsrud A Gursoy D Hardy C Harrison J H nin W Humphrey D Hurwitz A Hynninen N Jain N Krawetz S Kumar D Kunzman J Lai C Lee R McGreevy C Mei M Nelson J Phillips B Radak O Sarood A Shinozaki D Tanner D Wells G Zheng F Zhu Theoretical and Computational Biophysics Group Beckman Institute University of Illinois 1995 2011 The B
5. Acceptable Values decimal gt 0 0 Default Value 1 0 Description Scaling factor for electrostatic and van der Waals forces A value of 1 0 implies no modification of the interactions Any smaller value will lessen the nonbonded forces acting in the system vdwGeometricSigma lt use geometric mean to combine L J sigmas gt Acceptable Values yes or no 50 Default Value no Description Use geometric mean as required by OPLS rather than traditional arithmetic mean when combining Lennard Jones sigma parameters for different atom types e limitdist lt maximum distance between pairs for limiting interaction strength A gt Acceptable Values non negative decimal Default Value 0 Description The electrostatic and van der Waals potential functions diverge as the distance between two atoms approaches zero The potential for atoms closer than limitdist is instead treated as ar c with parameters chosen to match the force and potential at limitdist This option should primarily be useful for alchemical free energy perturbation calculations since it makes the process of creating and destroying atoms far less drastic energetically The larger the value of limitdist the more the maximum force between atoms will be reduced In order to not alter the other interactions in the simulation limitdist should be less than the closest approach of any non bonded pair of atoms 1 3 A appears to satisfy this for typical simulations but the user is enco
6. Default Value 2 Description Exponent for first boundary potential The only likely values to use are 2 and 4 e sphericalBCr2 lt radius for second boundary condition A gt Acceptable Values positive decimal Description Distance at which the second potential of the boundary conditions takes effect This distance is a radius from the center If this parameter is defined then spericalBCk2 must also be defined e sphericalBCk2 lt force constant for second potential gt Acceptable Values non zero decimal Description Force constant for the second harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center e sphericalBCexp2 lt exponent for second potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for second boundary potential The only likely values to use are 2 and 4 7 1 3 Cylindrical harmonic boundary conditions NAMD provides cylindrical harmonic boundary conditions These boundary conditions can consist of a single potential or a combination of two potentials The following parameters are used to define these boundary conditions e cylindricalBC lt use cylindrical boundary conditions gt Acceptable Values on or off Default Value off Description Specifies whether or not cylindrical boundary conditions are to be applied to the system If set to on then cylindricalBCCenter cylindricalBCr1 cylindricalBC1
7. Description The file containing histogram data is written on disk at the given time interval Like the ABF and metadynamics biases histogram uses parameters from the colvars to define its grid The grid ranges from lowerBoundary to upperBoundary and the bin width is set by the width parameter 10 5 7 Scripted biases Rather than using the biasing methods described above it is possible to apply biases provided at run time as a Tcl script in the spirit of TclForces e scriptedColvarForces lt Enable custom scripted forces on colvars gt Context global Acceptable Values boolean Default Value off Description If this flag is enabled a Tcl procedure named calc_colvar_forces accepting one parameter should be defined by the user It is executed at each timestep with the current step number as parameter between the calculation of colvars and the application of bias forces This procedure may use the scripting interface see 10 6 to access the values of colvars and apply forces on them effectively defining custom collective variable biases 10 6 Colvars scripting This interface is particularly useful to implement custom biases as scripted colvar forces See the scriptedColvarForces option in 10 5 7 Note that scripting commands may not be used directly in the NAMD configuration file before the first run or minimize statement They may be used either within the callback procedures e g calc_colvar forces or in the NAMD config file aft
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9. The fit itself is handled by the atom group object whose parameters are automatically set by the rmsd component For very specific applications however it may be useful to control the fitting process separately from the definition of the reference coordinates to evaluate various types of non minimal RMSD values This can be achieved by setting the related options refPositions etc explicitly in the atom group block This allows for the following non standard cases 1 applying the optimal translation but no rotation rotateReference off to bias or restrain the shape and orientation but not the position of the atom group 2 applying the optimal rotation but no translation translateReference off to bias or restrain the shape and position but not the orientation of the atom group 3 disabling the application of optimal roto translations which lets the RMSD component de cribe the deviation of atoms from fixed positions in the laboratory frame this allows for custom positional restraints within the colvars module 4 fitting the atomic positions to different reference coordinates than those used in the RMSD calculation itself 5 applying the optimal rotation and or translation from a separate atom group defined through refPositionsGroup the RMSD then reflects the deviation from reference coordinates in a separate moving reference frame 137 eigenvector projection of the atomic coordinates on a vector The block eigenvec
10. When set to hydrogen hydrogen atoms are kept on the same patch as their parents allowing faster distance checking and rigid bonds hgroupCutoff A lt used for group based distance testing gt Acceptable Values positive decimal Default Value 2 5 Description This should be set to twice the largest distance which will ever occur between a hydrogen atom and its mother Warnings will be printed if this is not the case This value is also added to the margin margin lt extra length in patch dimension A gt Acceptable Values positive decimal Default Value 0 0 Description An internal tuning parameter used in determining the size of the cubes of space with which NAMD uses to partition the system The value of this parameter will not change the physical results of the simulation Unless you are very motivated to get the very best possible performance just leave this value at the default pairlistMinProcs lt min procs for pairlists gt Acceptable Values positive integer Default Value 1 Description Pairlists may consume a large amount of memory as atom counts densities and cutoff distances increase Since this data is distributed across processors it is normally only problematic for small processor counts Set pairlistMinProcs to the smallest number of processors on which the simulation can fit into memory when pairlists are used pairlistsPerCycle lt regenerate x times per cycle gt Acceptable Values positive in
11. X Y Z 0 or B Default Value 0 Description Column of the PDB file to use for the containing fixed atom parameters for each atom The coefficients can be read from any floating point column of the PDB file A value of 0 indicates that the atom is not fixed 5 6 4 Extra bond angle and dihedral restraints Additional bond angle and dihedral energy terms may be applied to system allowing secondary or tertiary structure to be restrained for example Extra bonded terms are not considered part of the molecular structure and hence do not alter nonbonded exclusions The energies from extra bonded terms are included with the normal bond angle and dihedral energies in NAMD output All extra bonded terms are harmonic potentials of the form U x k 1x 2 ye except dihedrals and impropers with a non zero periodicity specified which use U x k 1 cos nx tref The only difference between dihedrals and impropers is the output field that their potential energy is added to The extra bonded term implementation shares the parallel implementation of regular bonded terms in NAMD allowing large numbers of extra terms to be specified with minimal impact on parallel scalability Extra bonded terms do not have to duplicate normal bonds angles dihedrals but each extra bond angle dihedral should only involve nearby atoms If the atoms involved are too far apart a bad global bond count will be reported in parallel runs Extra bonded terms are enabled
12. centers of mass of groups of atoms are needed In addition information must be requested one timestep in advance To apply forces individually to a potentially large number of atoms use tc1BC instead as described in Sec 9 11 The following configuration parameters are used to enable the Tcl interface e tclForces lt is Tcl interface active gt Acceptable Values on or off Default Value off Description Specifies whether or not Tcl interface is active If it is set to off then no Tcl code is executed If it is set to on then Tcl code specified in tclForcesScript parameters is executed e tclForcesScript lt input for Tcl interface gt Acceptable Values file or script Description Must contain either the name of a Tcl script file or the script itself between and may include multiple lines This parameter may occur multiple times and scripts will be executed in order of appearance The script s should perform any required initialization 105 on the Tcl interpreter including requesting data needed during the first timestep and define a procedure calcforces to be called every timestep At this point only low level commands are defined In the future this list will be expanded Current commands are e print lt anything gt This command should be used instead of puts to display output For example print Hello World e atomid lt segname gt lt resid gt lt atomname gt Determines atomid of an atom from its
13. dimensionless and of commensurate size For instance setting a scaled force constant of 157 10 kcal mol acting on two colvars an angle with a width of 5 degrees and a distance with a width of 0 5 A will apply actual force constants of 0 4 kcal molxdegree for the angle and 40 kcal mol for the distance e centers lt Initial harmonic restraint centers gt Context harmonic Acceptable Values space separated list of colvar values Description The centers equilibrium values of the restraint are entered here The number of values must be the number of requested colvars Each value is a decimal number if the corresponding colvar returns a scalar a x y z triplet if it returns a unit vector or a vector and a q0 q1 q2 q3 quadruplet if it returns a rotational quaternion If a colvar has periodicities or symmetries its closest image to the restraint center is considered when calculating the harmonic potential Tip A complex set of restraints can be applied to a system by defining several colvars and applying one or more harmonic restraints to different groups of colvars In some cases dozens of colvars can be defined but their value may not be relevant to limit the size of the colvars trajectory file it may be wise to disable outputValue for such ancillary variables and leave it enabled only for relevant ones Moving restraints steered molecular dynamics The following options allow to change gradual
14. gt Acceptable Values on or off Default Value off Description Turns slow energy minimization on or off e maximumMove lt maximum distance an atom can move during each step A gt Acceptable Values positive decimal Default Value 0 75 x cutoff stepsPerCycle Description Maximum distance that an atom can move during any single timestep of minimization This is to insure that atoms do not go flying off into space during the first few timesteps when the largest energy conflicts are resolved 7 3 Dynamics 7 3 1 Timestep parameters e numsteps lt number of timesteps gt Acceptable Values positive integer 76 Description The number of simulation timesteps to be performed An integer greater than 0 is acceptable The total amount of simulation time is numsteps x timestep e timestep lt timestep size fs gt Acceptable Values non negative decimal Default Value 1 0 Description The timestep size to use when integrating each step of the simulation The value is specified in femtoseconds e firsttimestep lt starting timestep value gt Acceptable Values non negative integer Default Value 0 Description The number of the first timestep This value is typically used only when a simulation is a continuation of a previous simulation In this case rather than having the timestep restart at 0 a specific timestep number can be specified 7 3 2 Initialization e temperature lt initial temperature K gt Acceptable Value
15. structure files in X PLOR PSF format and energy parameter files in either CHARMM or X PLOR formats Output formats include PDB coordinate files and binary DCD trajectory files These similar ities assure that the molecular dynamics trajectories from NAMD can be read by CHARMM or X PLOR and that the user can exploit the many analysis algorithms of the latter packages e Dynamics Simulation Options MD simulations may be carried out using several options including Constant energy dynamics Constant temperature dynamics via Velocity rescaling Velocity reassignment Langevin dynamics Periodic boundary conditions Constant pressure dynamics via Berendsen pressure coupling Nos Hoover Langevin piston Energy minimization Fixed atoms 13 Rigid waters Rigid bonds to hydrogen Harmonic restraints Spherical or cylindrical boundary restraints e Easy to Modify and Extend Another primary design objective for NAMD is extensibility and maintainability In order to achieve this it is designed in an object oriented style with C Since molecular dynamics is a new field new algorithms and techniques are continually being developed NAMD s modular design allows one to integrate and test new algorithms easily If you are contemplating a particular modification to NAMD you are encouraged to contact the developers for guidance e Interactive MD simulations A system undergoing simulati
16. tag gt lt column of PDB from which to read atom charges gt Acceptable Values X Y Z O or B Default Value Atom charge used for electrostatics Description Which column in the PDB file specified by mgridforcefile contains the atom charge By default the charge value specified for the short range Columb interactions are also used for the grid force Both mgridforcecol and mgridforceqcol can be specified in which case the apparent charge of the atom will be the product of the two values mgridforcepotfile lt tag gt lt grid potential file name gt Acceptable Values UNIX file name Description File specifying the grid size coordinates and potential values mgridforcevolts lt tag gt lt grid potential units in eV charge gt Acceptable Values yes or no Default Value no Description If set the grid potential values are expressed in eV Otherwise values are in kcal mol charge mgridforcescale lt tag gt lt scale factor for grid potential gt Acceptable Values Vector of decimals scale scale scale Default Value 111 Description Scale factor applied to the grid potential values mgridforcecont1 lt tag gt lt Is grid continuous in the direction of the first basis vector gt Acceptable Values yes or no 95 Default Value no Description By specifying that the grid is continuous in a direction atoms outside of the grid will be affected by a force determined by interpolating based on the values at
17. yes Description PARM file explicitly gives complete exclusion including 1 4 exclusions information When readexclusions is set to on NAMD will read all exclusions from PARM file and will not add any more alternatively if readexclusions is set to off NAMD will ignore the exclusions in PARM file and will automatically generate them according to the exclusion policy specified by exclude e scnb lt VDW 1 4 scaling factor gt Acceptable Values decimal gt 1 0 Default Value 2 0 Description Same meaning as SCNB in AMBER Note that in NAMD 1 4 vdw inter actions are DIVIDED by scnb whereas 1 4 electrostatic interactions are MULTIPLIED by 1 4scaling So 1 4scaling should be set to the inverse of SCEE value used in AMBER Caveat 1 Polarizable parameters in AMBER are not supported 2 NAMD does not support the 10 12 potential terms in some old AMBER versions When non zero 10 12 parameter is encountered in PARM file NAMD will terminate 3 NAMD has several exclusion policy options defined by exclude The way AMBER dealing with exclusions corresponds to the scaled1 4 in NAMD So for simulations using AMBER force field one would specify exclude scaled1 4 in the configuration file and set 1 4scaling to the inverse value of SCEE as would be used in AMBER 28 4 NAMD does not read periodic box lengths in PARM or coordinate file They must be explicitly specified in NAMD configuration file 5 By default NAMD applies swit
18. 000000e 00 0 000000e 00 13 99 0 000000e 00 0 000000e 00 TYPE SISI O 0 000000e 00 0 000000e 00 0 01 0 000000e 00 0 000000e 00 13 98 0 000000e 00 0 000000e 00 13 99 0 000000e 00 0 000000e 00 The following three parameters are required for tabulated energies e tabulatedEnergies lt use tabulated energies gt Acceptable Values yes or no Default Value no Description Specifies whether or not tabulated energies will be used for van der Waals interactions between specified pairs of atom types e tabulatedEnergiesFile lt file containing energy table gt Acceptable Values file name Description Provides one energy table for each interaction type in parameter file See format above 57 e tableInterpType lt cubic or linear interpolation gt Acceptable Values cubic or linear Description Specifies the order for interpolating between energy table entries 5 3 Water Models NAMD currently supports the 3 site TIP3P water model the 4 site TIP4P water model and the 5 site SWM4 NDP water model from the Drude force field 44 TIP3P is the current default water model Usage of alternative water models is described below e waterModel lt using which water model gt Acceptable Values tip3 tip4 swm4 Default Value tip3 Description Specifies the water model to be used When using the TIP3P water model the ordering of atoms within each TIP3P water molecule must be oxygen hydrogen hydro gen When using the TIP4P water
19. 36 NAMD configuration file for BPTI molecular system structure output bpti psf force field paratypecharmm on parameters toppar par_al122_prot inp exclude scaled1 4 1 4scaling 1 0 approximations switching on switchdist 8 cutoff 12 pairlistdist 13 5 margin 0 stepspercycle 20 integrator timestep 1 0 output outputenergies 10 outputtiming 100 binaryoutput no molecular system coordinates output bpti pdb output outputname output bpti dcdfreq 1000 protocol temperature 0 reassignFreq 1000 reassignTemp 25 reassignIncr 25 reassignHold 300 script minimize 1000 run 20000 37 4 3 Building solvent around a protein The following script illustrates how psfgen and VMD can be used together to add water around a protein structure It assumes you already have a psf and pdb file for your protein as well as a box of water which is large enough to contain the protein For more information on how atomselections can be used within VMD scripts see the VMD User s Guide proc addwater psffile pdbfile watpsf watpdb Create psf pdb files that contain both our protein as well as a box of equilibrated water The water box should be large enough to easily contain our protein resetpsf readpsf psffile pdb pdbfile readpsf watpsf pdb watpdb Load the combined structure into VMD writepsf combine psf writepdb combine pdb mol load psf combine psf pdb combine pdb Assume that the segid o
20. Accelerated Molecular Dynamics o 12 1 1 Theoretical background e 12 1 2 NAMD parameters s sacs oo cacaraca a Re ee ee es 12 2 Adaptive Tempering sosai aor a naa E a A oe a 12 2 1 NAMD parameters 12 3 Locally enhanced sampling 12 3 1 Structure generation osos e A a A eS 123 2 Simulation a taa A e A BA See 12 4 Replica exchange simulations e 12 5 Random acceleration molecular dynamics simulations 13 Structure based simulations 13 1 Hybrid MD Go Simulation 13 1 1 Hybrid MD Go model o s so es a a pee 020000000 n a ee ee 13 1 2 Hybrid MD Go considerations 2 2 2 ee 13 1 3 Configuration file modifications 2 0 2 0 0 02000002 eee 13 1 4 GoParameter format 13 2 Running SMOG simulations ee 13 2 1 SMOG model considerations 0000 eee ee 13 2 2 Configuration file modifications 2 2 0 0 02 ee ee ee 14 Runtime Analysis 14 1 Pair interaction calculations o oo oa ee 14 2 Pressure profile calculations ooo ee 15 Translation between NAMD and X PLOR configuration parameters 16 Sample configuration files 17 Running NAMD 17 1 Individual Windows Linux Mac OS X or Other Unix Workstations 17 2 Windows Clusters and Workstation Networks o 00005 17 3 Linux Clusters with InfiniBand or Other High Performance Networks 165 165 165 166 167 168 171 173 173 173 175 175 175 176 177
21. Acceptable Values positive integer Default Value 1 Description The number of timesteps between each energy output of NAMD This value specifies how often NAMD should output the current energy values to stdout which can be redirected to a file By default this is done every step For long simulations the amount of output generated by NAMD can be greatly reduced by outputting the energies only occasionally e mergeCrossterms lt add crossterm energy to dihedral gt Acceptable Values yes or no Default Value yes Description If crossterm or CMAP terms are present in the potential the energy is added to the dihedral energy to avoid altering the energy output format Disable this feature to add a separate CROSS field to the output e outputMomenta lt timesteps between momentum output gt Acceptable Values nonnegative integer Default Value 0 Description The number of timesteps between each momentum output of NAMD If specified and nonzero linear and angular momenta will be output to stdout e outputPressure lt timesteps between pressure output gt Acceptable Values nonnegative integer Default Value 0 Description The number of timesteps between each pressure output of NAMD If specified and nonzero atomic and group pressure tensors will be output to stdout e outputTiming lt timesteps between timing output gt Acceptable Values nonnegative integer Default Value the greater of firstLdbStep or 10x outputEnergies
22. Control and Equilibration o e e 7 4 1 Langevin dynamics parameters e 7 4 2 Temperature coupling parameters 2 0 000200048 7 4 3 Temperature rescaling parameters 0 00000 eee 7 4 4 Temperature reassignment parameters 2 00 005 7 4 5 Lowe Andersen dynamics parameters 0 2 0 00000004 Pressure Control td eA gies A He oe te ea ie ee Bae 7 5 1 Berendsen pressure bath coupling 222004 7 5 2 Nos Hoover Langevin piston pressure control 0 00 Performance Tuning 8 1 Non bonded interaction distance testing 0 0 20 0000 66 66 66 66 66 69 70 72 72 72 73 74 79 75 76 76 76 TT 78 78 80 80 81 81 82 82 83 84 85 88 9 User Defined Forces 92 9 1 Constant Forces a A Se ee a ee ee ae 92 9 2 External Electric Field 2 2 ee ee 92 9 3 Grid Forces cisco a eee hate gah ee ee a ete 93 9 4 Moving Constraints 4 28 4 a e ee a ee eee ee 96 9 5 Rotating Constraints sc so 4 dos sled eee gs Abaco A os er ee A AA 98 9 6 Symmetry Restraints ee 99 9 7 Targeted Molecular Dynamics TMD 101 9 8 Steered Molecular Dynamics SMD o e 103 9 9 Interactive Molecular Dynamics IMD AA 104 9 10 Tcl Forces and Analysis pan a ang aa pa nap e Ea a Na er ON 105 9 11 Tel Boundary Forces ut bate eens Boe Ra Re Be ah
23. Currently the only available method is the impulse based Verlet I or r RESPA method which is stable for timesteps up to 4 fs for long range electrostatic forces 2 fs for short range nonbonded forces and 1 fs for bonded forces Setting rigid all i e using SHAKE increases these timesteps to 6 fs 2 fs and 2 fs respectively but eliminates bond motion for hydrogen The mollified impulse method MOLLY reduces the resonance which limits the timesteps and thus increases these timesteps to 6 fs 2 fs and 1 fs while retaining all bond motion e fullElectFrequency lt number of timesteps between full electrostatic evaluations gt Acceptable Values positive integer factor of stepspercycle Default Value nonbondedFreq 78 Description This parameter specifies the number of timesteps between each full elec trostatics evaluation It is recommended that fullElectFrequency be chosen so that the product of fullElectFrequency and timestep does not exceed 4 0 unless rigidBonds all or molly on is specified in which case the upper limit is perhaps doubled e nonbondedFreq lt timesteps between nonbonded evaluation gt Acceptable Values positive integer factor of fullElectFrequency Default Value 1 Description This parameter specifies how often short range nonbonded interactions should be calculated Setting nonbondedFreq between 1 and fullElectFrequency allows triple timestepping where for example one could evaluate bonded forces every 1 fs short ra
24. Description The number of timesteps between each timing output of NAMD If nonzero CPU and wallclock times and memory usage will be output to stdout These data are from node 0 only CPU times and memory usage for other nodes may vary 27 3 3 AMBER force field parameters AMBER format PARM file and coordinate file can be read by NAMD which allows one to use AMBER force field to carry out all types of simulations that NAMD has supported NAMD can read PARM files in either the format used in AMBER 6 or the new format defined in AMBER 7 The output of the simulation restart file DCD file etc will still be in traditional format that has been used in NAMD e amber lt use AMBER format force field gt Acceptable Values yes or no Default Value no Description If amber is set to on then parmfile must be defined and structure and parameters should not be defined e parmfile lt AMBER format PARM file gt Acceptable Values UNIX filename Description This file contains complete topology and parameter information of the system e ambercoor lt AMBER format coordinate file gt Acceptable Values UNIX filename Description This file contains the coordinates of all the atoms Note that coordinates can also be used for PDB format coordinate file When amber is set to on either ambercoor or coordinates must be defined but not both e readexclusions lt Read exclusions from PARM file gt Acceptable Values yes or no Default Value
25. Parameter restartname X PLOR Parameter SAVE Filename prefix for the restart files NAMD Parameter restartfreq X PLOR Parameter ISVFrq Number of timesteps between the generation of restart files NAMD Parameter DCDfile X PLOR Parameter TRAJectory Filename for the position trajectory file NAMD Parameter DCDfreq X PLOR Parameter NSAVC Number of timesteps between writing coordinates to the trajectory file NAMD Parameter velDCDfile X PLOR Parameter VELOcity Filename for the velocity trajectory file NAMD Parameter velDCDfreq X PLOR Parameter NSAVV Number of timesteps between writing velocities to the trajectory file NAMD Parameter numsteps X PLOR Parameter NSTEp Number of simulation timesteps to perform 197 16 Sample configuration files This section contains some simple example NAMD configuration files to serve as templates This file shows a simple configuration file for alanin It performs basic dynamics with no output files or special features protocol params numsteps 1000 initial config coordinates alanin pdb temperature 300K seed 12345 output params outputname tmp alanin binaryoutput no integrator params timestep 1 0 force field params structure alanin psf parameters alanin params exclude scaled1 4 1 4scaling 1 0 switching on switchdist 8 0 cutoff 12 0 pairlistdist 13 5 stepspercycle 20 198 This file is again for alanin but shows a slightly mo
26. Reading coordinates from the PDB files 32 6 Deleting unwanted atoms such as overlapping water molecules 7 Guessing missing coordinates of hydrogens and other atoms 8 Writing PSF and PDB files for use in NAMD 4 1 1 Preparing separate PDB files Many PDB files in the PDB databank contain multiple chains corresponding to protein subunits water and other miscellaneous groups Protein subunits are often identified by their chain ID in the PDB file In psfgen each of these groups must be assigned to their own segment This applies most strictly in the case of protein chains each of which must be assigned to its own segment so that N terminal and C terminal patches can be applied You are free to group water molecules into whatever segments you choose Chains can be split up into their own PDB files using your favorite text editor and or Unix shell commands as illustrated in the BPTI example below If you are using VMD you can also use atom selections to write pieces of the structure to separate files Split a file containing protein and water into separate segments Creates files named myfile_water pdb myfile_frag0 pdb myfile_fragi pdb Requires VMD mol load pdb myfile pdb set water atomselect top water water writepdb myfile_water pdb set protein atomselect top protein set chains lsort unique protein get pfrag foreach chain chains set sel atomselect top pfrag chain sel writepdb myfile_frag chain p
27. Tcl procedures calc_ lt scriptedFunction gt and calc_ lt scriptedFunction gt gradient both accepting as many parameters as the colvar has components Values of the components will be passed to 145 those procedures in the order defined by their sorted name strings Note that if all components are of the same type their default names are sorted in the order in which they are defined so that names need only be specified for combinations of components of different types calc_ lt scriptedFunction gt should return one value of type lt scriptedFunctionType gt cor responding to the colvar value calc_ lt scriptedFunction gt gradient should return a Tcl list containing the derivatives of the function with respect to each component If both the function and some of the components are vectors the gradient is really a Jacobian ma trix that should be passed as a linear vector in row major order i e for a function f Vili Vefo ear e scriptedFunctionType lt Type of value returned by the scripted colvar gt Context colvar Acceptable Values string Default Value scalar Description If a colvar is defined as a scripted function its type is not constrained by the types of its components With this flag the user may specify whether the colvar is a scalar or one of the following vector types vector3 a 3D vector unit_vector3 a normalized 3D vector or unit_quaternion a normalized quaternion or vector a vector whose size is specifi
28. a collective variables configuration Dual topology description for an alchemical simulation Case example of the muta tion of alanine into serine The lighter color denotes the non interacting alternate Slate he Goa A wo ten a Ra tt ee al ee ee Ba et ee a ee Le Ts Convergence of an FEP calculation If the ensembles representative of states a and b are too disparate equation 59 will not converge a If in sharp contrast the configurations of state b form a subset of the ensemble of configurations characteristic of state a the simulation is expected to converge b The difficulties reflected in case a may be alleviated by the introduction of mutually overlapping intermediate states that connect a to b c It should be mentioned that in practice the kinetic contribution 7 p is assumed to be identical for state a and state b Relationship of user defined A to coupling of electrostatic or vdW interactions to a simulation given specific values of alchElecLambdaStart or alchVdwLambdaEnd Sample TI data log 22 against A The blue shaded area shows the integral with fine sampling close to the end point The red area shows the difference when A values are more sparse In this example insufficient sampling before A 20 1 can result in a large overestimation of the integral Beyond 20 2 sparser sampling is justified as dE dA is not changing quickly roda tl ts a a BO Schematics of the aMD method When the original po
29. adjacent residues can be defined within a chaintype Each additional new restriction is given on its own line Each pairwise chaintype should be written in its own block of text with each entry given its own line It is recommended that individual pairwise potential be separated by a blank line 13 2 Running SMOG simulations 13 2 1 SMOG model considerations NAMD supports the SMOG model from published from Onuchic s lab 77 78 The input files for SMOG can be generated from the SMOG website http smog server org 54 It is recommended to run these simulations with 1 4 exclusions as opposed to scaled 1 4 a 0 5fs timestep and with a 0 5fs timestep as described in 77 78 13 2 2 Configuration file modifications As the SMOG model uses GROMACS topology and coordinate files the GROMACS configura tion parameters gromacs grotopfile grocoorfile must be defined The description for the GROMACS configuration parameters are reproduced below e gromacs lt use GROMACS format force field gt Acceptable Values on or off Default Value off Description If gromacs is set to on then grotopfile must be defined and structure and parameters should not be defined e grotopfile lt GROMACS format topology parameter file gt Acceptable Values UNIX filename Description This file contains complete topology and parameter information of the system 189 e grocoorfile lt GROMACS format coordinate file gt Acceptable Values
30. allows the colvar module to identify this colvar unambiguously it is also used in the trajectory file to label to the columns corresponding to this colvar e width lt Colvar fluctuation scale or resolution for grid based methods gt Context colvar Acceptable Values positive decimal Default Value 1 0 Description This number has the same physical unit as the colvar value and defines an effective colvar unit Biasing algorithms use it for different purposes Harmonic restraints 10 5 3 use it to set the physical unit of the force constant which is useful for multidimen sional restraints involving colvars with different units or scale which may then be defined by a single scaled force constant Histogram 10 5 6 and ABF biases 10 5 1 interpret it as the grid spacing in the direction of this variable Metadynamics 10 5 2 uses it to set the width of newly added hills In other cases it is simplest to keep the default value of 1 so that harmonic force constants are provided in their usual physical unit When a non unity width is required by the application the optimal value is application dependent but can often be thought of as a user provided estimate of the fluctuation amplitude for the colvar In those cases it should generally be set smaller than or equal to the standard deviation of the colvar during a very short simulation run e lowerBoundary lt Lower boundary of the colvar gt Context colvar Acceptable Values decimal De
31. and PDB files Compare to topology alias above in which the alias is is used as the residue name in generated files This command also exists under the deprecated name alias Arguments lt alternate name gt Residue name found in PDB file 39 lt real name gt Residue name found in topology file or aliases Context Before reading sequence with pdb May call multiple times segment segids resids residue first last lt segment ID gt resid atom name lt commands gt Purpose Build a segment of the molecule A segment is typically a single chain of protein or DNA with default patches applied to the termini Segments may also contain pure solvent or lipid Options segids resids residue first last are used to query information about the specified segment Arguments segids Return a list of segids for the molecule in the current context resids Return a list of resids for the molecule in the current context residue Return the residue name of the residue in the given segment with the given resid atoms Return a list of atoms for the given segment with the given resid coordinates Return x y z coordinates for the given atom first Returns the name of the patch that was applied to the beginning of the specified segment last Returns the name of the patch that was applied to the end of the specified segment lt segment ID gt Unique name for segment 1 4 characters lt commands gt Sequence of co
32. and post processing The following options may be useful only for applications that go beyond the calculation of a PMF by metadynamics e name lt Name of this metadynamics instance gt Context metadynamics 156 Acceptable Values string Default Value meta rank number Description This option sets the name for this metadynamics instance While it is not advisable to use more than one metadynamics instance within the same simulation this allows to distinguish each instance from the others If there is more than one metadynamics instance the name of this bias is included in the metadynamics output file names such as e g the pmf file e keepHills lt Write each individual hill to the state file gt Context metadynamics Acceptable Values boolean Default Value off Description When useGrids and this option are on all hills are saved to the state file in their analytic form alongside their grids This makes it possible to later use exact analytic Gaussians for rebinGrids To only keep track of the history of the added hills writeHillsTrajectory is preferable e writeHillsTrajectory lt Write a log of new hills gt Context metadynamics Acceptable Values boolean Default Value on Description If this option is on a logfile is written by the metadynamics bias with the name outputName colvars lt name gt hills traj which can be useful to follow the time series of the hills When multipleReplicas is on its n
33. and the values of H are 0 0 1 2155 1 2 Tu Bis fis I Sra E Pi a ee Fis 2 1n 2 Pos Pj po pe TL te apis bse d e Tij Tij 2 re E r2 TN 1 Pjs Tij Pjs Hij HI 2 r s 7 rig tPjs 1 1 1 2 2 _ 2 1 1 Pio IV 3 Pio 2 Eo n Pio p rij tPjs Tij In Tij Pjs V 1 Pjs ln Pis Tij 2 ij Ps aa ay E Tij Pjs VI 0 18 Below are defined the derivatives of the above functions which are required for force calculations OEij _ k ao enpatia Orij fij Orij fh Ori OD oR gt Of Orij s expide Orij O fij zi Tij 1 r Ori o fij i 1E E d a d TEE E 1 tanh Bb BYR VWF 8 2910 3008 T ij d k dH drij w po 2 drij KEN OH dry 7 Pro 2 Orn drij OH OA A OK bu OF bi k d api 7 Sk P 1 tanh Sui Bu y8 6 284 360 La dri Pi zi a j ig Ue 1 tanh 5 py 703 5 281 3047 Se BH OF 1 keqiqj Dij a a e am aa ca LRE exp k fij Diz Qa i ex ri da T Qj 2 j Es E bs fij i 4 a 400 68 19 20 21 22 23 24 25 26 27 28 retpjs Tij Te pPjst raj Ps r 1_ jy T22 Br2r2 2 a MA rerij 0js i5 Tij 3 5 7 9 11 p3 Pp pi PS P dat 60 8c 10d 120 _ sa NR mna O ij ij 1 2 aj oe 2 2 SEE a Pal yte is 1 In i Lis 29 Orij rij r303 2ri Tit Pie 2 2 2 21 59 2 2 2 tv 2 Teas r
34. another e loweAndersenRate lt rate for Lowe Andersen collisions 1 ps gt Acceptable Values positive decimal Default Value 50 Description Determines the probability of a collision between atoms within the cutoff radius The probability is the rate specified by this keyword times the non bonded timestep 7 5 Pressure Control Constant pressure simulation and pressure calculation require periodic boundary conditions Pres sure is controlled by dynamically adjusting the size of the unit cell and rescaling all atomic coordi nates other than those of fixed atoms during the simulation Pressure values in NAMD output are in bar PRESSURE is the pressure calculated based on individual atoms while GPRESSURE incorporates hydrogen atoms into the heavier atoms to which they are bonded producing smaller fluctuations The TEMPAVG PRESSAVG and GPRESSAVG are the average of temperature and pressure values since the previous ENERGY output for the first step in the simulation they will be identical to TEMP PRESSURE and GPRESSURE The phenomenological pressure of bulk matter reflects averaging in both space and time of the sum of a large positive term the kinetic pressure nRT V and a large cancelling negative term the static pressure The instantaneous pressure of a simulation cell as simulated by NAMD will have mean square fluctuations according to David Case quoting Section 114 of Statistical Physics by Landau and Lifshitz of kT V 8 wh
35. applied to the system If set to on then rotConsAxis rotConsPivot and rotConsVel must be defined May not be used with movingConstraints e rotConsAxis lt Axis of rotation gt Acceptable Values vector may be unnormalized 98 9 6 Description Axis of rotation Can be any vector It gets normalized before use If the vector is 0 no rotation will be performed but the calculations will still be done rotConsPivot lt Pivot point of rotation gt Acceptable Values position in A Description Pivot point of rotation The rotation axis vector only gives the direction of the axis Pivot point places the axis in space so that the axis goes through the pivot point rotConsVel lt Angular velocity of rotation gt Acceptable Values rate in degrees per timestep Description Angular velocity of rotation degrees timestep Symmetry Restraints Symmetry restraints are based on symmetrical relationships between monomers Defined monomers are transformed to overlap and an average position for each atom is calculated After the average structure is transformed back a harmonic force is calculated which drives each monomer to the average symmetryRestraints lt Are symmetry restraints active gt Acceptable Values on or off Default Value off Description Should Symmetry constraining forces be applied to the system If symmetry restraints are enabled symmetryk and symmetryFile must be defined in the input file as well See s
36. at which force samples are synchronized among the replicas gt Context abf Acceptable Values positive integer Default Value outputFreq Description Inthe current implementation of shared ABF each replica maintains a sepa rate buffer of system force samples that determine the biasing force Every sharedFreq steps the replicas communicate the samples that have been gathered since the last synchronization time ensuring all replicas apply a similar biasing force Output files The ABF bias produces the following files all in multicolumn ASCII format e outputName grad current estimate of the free energy gradient grid in multicolumn e outputName count total number of samples collected on the same grid e outputName pmf only for one dimensional calculations integrated free energy profile or PMF If several ABF biases are defined concurrently their name is inserted to produce unique filenames for output as in outputName abf1 grad This should not be done routinely and could lead to meaningless results only do it if you know what you are doing If the colvar space has been partitioned into sections windows in which independent ABF sim ulations have been run the resulting data can be merged using the inputPrefix option described above a run of 0 steps is enough Post processing reconstructing a multidimensional free energy surface If a one dimensional calculation is performed the estimated free energy gradient is automaticall
37. atoms involved in the force measurement on do not participate in the definition of This can be obtained using the option oneSiteSystemForce of the distance angle and dihedral components example Ramachandran angles 4 e and are orthogonal by construction Useful cases are the sum and difference of two components or distance_z and distance_xy using the same axis 4 Mutual orthogonality of components when several components are combined into a colvar it is assumed that their vectors v equation 53 are mutually orthogonal The cases described for colvars in the previous paragraph apply 5 Orthogonality of colvars and constraints equation 52 can be satisfied in two simple ways if either no constrained atoms are involved in the force measurement see point 3 above or pairs of atoms joined by a constrained bond are part of an atom group which only intervenes through its center center of mass or geometric center in the force measurement In the latter case the contributions of the two atoms to the left hand side of equation 52 cancel out For example all atoms of a rigid TIP3P water molecule can safely be included in an atom group used in a distance component 148 Parameters for ABF ABF depends on parameters from collective variables to define the grid on which free energy gradients are computed In the direction of each colvar the grid ranges from lowerBoundary to upperBoundary and the bin width grid spacin
38. atomsColValue colvars atom group keyword 126 atomsFile colvars atom group keyword 126 auto psfgen command 40 axis colvars distanceZ distanceXY keyword 132 axis colvars inertiaZ keyword 139 axis colvars tilt spinAngle keyword 141 Bad global exclusion count 89 BerendsenPressure parameter 17 84 BerendsenPressureCompressibility parame ter 17 85 BerendsenPressureFreq parameter 85 BerendsenPressureRelaxationTime ter 17 85 BerendsenPressureTarget parameter 17 85 biasTemperature colvars metadynamics key word 155 binaryoutput parameter 17 25 binaryrestart parameter 25 bincoordinates parameter 24 binvelocities parameter 24 BOUNDARY energy 26 parame callback command 16 cellBasisVectorl parameter 72 cellBasisVector2 parameter 72 cellBasisVector3 parameter 72 cellOrigin parameter 72 centerReference colvars atom group keyword 127 centers colvars alb keyword 161 centers colvars harmonic keyword 158 centers colvars linear keyword 161 checkpoint command 17 checkpointFree command 17 19 checkpointLoad command 17 19 checkpointStore command 17 19 checkpointSwap command 17 19 closestToQuaternion colvars orientation keyword 140 colvars colvars colvar bias keyword 146 colvars colvars NAMD configuration file key word 114 colvarsConfig colvars NAMD configuration file keyword 114 colvarsInput colvars NAMD configuration file keyword 115 colvarsRestartFrequency colv
39. built e regenerate angles dihedrals Purpose Remove all angles and or dihedrals and completely regenerate them using the segment automatic generation algorithms This is only needed if patches were applied that do not correct angles and bonds Segment and file defaults are ignored and angles dihedrals for the entire molecule are regenerated from scratch Arguments angles Enable generation of angles from bonds dihedrals Enable generation of dihedrals from angles Context After one or more segments have been built e regenerate resids Purpose Remove insertion codes and minimally modify resids to retain uniqueness No modifications will be made in segments that have monotonically increasing resids and do not contain insertion codes Within a segment no modifications will be made to residues preceeding the first non increasing resid or residue with an insertion code Arguments resids Enable regeneration of resids to remove insertion codes Context After one or more segments have been built e multiply lt factor gt lt segid resid atomnamel gt Purpose Create multiple images of a set of atoms for use in locally enhanced sampling The beta column of the output pdb file is set to 1 lt factor gt for each image Multiple copies of bonds angles etc are created Atom residue or segment names are not altered images are distinguished only by beta value This is not a normal molecular structure and may confuse other tool
40. but may be faster in certain cases In the above example one could specify devices 0 2 0 2 to cause device 0 to be shared by threads 0 and 2 etc When running on multiple nodes the devices specification is applied to each physical node separately and there is no way to provide a unique list for each node GPUs of compute capability 1 0 are no longer supported and are ignored GPUs with two or fewer multiprocessors are ignored unless specifically requested with devices While charmrun with local will preserve LD_LIBRARY_PATH normal charmrun does not You can use charmrun runscript to add the namd2 directory to LD_LIBRARY_PATH with the following executable runscript 208 bin csh setenv LD_LIBRARY_PATH 1 h LD_LIBRARY_PATH x For example charmrun runscript runscript p24 namd2 ppn 3 lt configfile gt An InfiniBand network is highly recommended when running CUDA accelerated NAMD across multiple nodes You will need either an ibverbs NAMD binary available for download or an MPI NAMD binary must build Charm and NAMD as described above to make use of the InfiniBand network The use of SMP binaries is also recommended when running on multiple nodes with one process per GPU and as many threads as available cores reserving one core per process for the communication thread The CUDA NVIDIA s graphics processor programming platform code in NAMD is completely self contained and does not use any of the CUDA suppor
41. by group Each group is identified by a name that is unique in the context of the specific colvar component e g for a distance component the names of the two groups are group1 and group2 The name is followed by a brace delimited block of selection keywords these may be used individually or in combination with each other and each can be repeated any number of times Selection is incremental each keyword adds the corresponding atoms to the selection so that different sets of atoms can be combined However atoms included by multiple keywords are only counted once Below is an example configuration for an atom group named atoms which uses an unusually varied combination of selection keywords atoms add atoms 1 and 3 to this group note the first atom in the system is 1 atomNumbers 13 add atoms starting from 20 up to and including 50 atomNumbersRange 20 50 add index group requires a ndx file to be provided globally indexGroup Water add all the atoms with occupancy 2 in the file atoms pdb atomsFile atoms pdb atomsCol O atomsColValue 2 0 add all the C alphas within residues 11 to 20 of segments PR1 and PR2 psfSegID PR1 PR2 atomNameResidueRange CA 11 20 atomNameResidueRange CA 11 20 The resulting selection includes atoms 1 and 3 those between 20 and 50 and those in the index group called Water the indices of this group are read from the file provided by indexFile in the global section
42. case the force constant k controls the potential parallel to the pulling direction 7 while the transverse force constant k controls the potential perpendicular to Output NAMD provides output of the current SMD data The frequency of output is specified by the SMDOutputFreq parameter in the configuration file Every SMDOutputFreq timesteps NAMD will print the current timestep current position of the center of mass of the restrained atoms and the current force applied to the center of mass in piconewtons pN The output line starts with word SMD 103 Parameters The following parameters describe the parameters for the SMD feature of NAMD 9 9 SMD lt Are SMD features active gt Acceptable Values on or off Default Value off Description Should SMD harmonic constraint be applied to the system If set to on then SMDk SMDFile SMDVel and SMDDir must be defined Specifying SMDOutputFreq is optional SMDFile lt SMD constraint reference position gt Acceptable Values UNIX filename Description File to use for the initial reference position for the SMD harmonic constraints All atoms in this PDB file with a nonzero value in the occupancy column will be tagged as SMD atoms The coordinates of the tagged SMD atoms will be used to calculate the initial center of mass During the simulation this center of mass will move with velocity SMDVel in the direction SMDDir The actual atom order in this PDB file must match that in the stru
43. distributions are available 18 2 Platforms on which NAMD will currently run NAMD should be portable to any parallel platform with a modern C compiler to which Charm and Converse have been ported Precompiled NAMD CVS 2015 12 17 binaries are available for download for the following platforms e Windows XP etc on x86 or x86 64 processors e Mac OS X on Intel processors e Linux on x86 or x86 64 processors e Linux on x86 64 processors with NVIDIA GPUs CUDA NAMD may be compiled for the following additional platforms e Cray XT XE XK XC e IBM Blue Gene L P Q e Linux or AIX on POWER processors e Linux on ARM processors e Linux on ARM or POWER processors with NVIDIA GPUs CUDA e Linux on x86 64 processors with Intel Xeon Phi coprocessors MIC e Solaris on x86 64 processors 18 3 Installing NAMD A NAMD binary distribution need only be untarred or unzipped and can be run directly in the resulting directory When building from source code make release will generate a self contained directory and tar gz or zip archive that can be moved to the desired installation location Windows and CUDA builds include Tcl dll and CUDA so files that must be in the dynamic library path 211 18 4 Compiling NAMD We provide complete and optimized binaries for all common platforms to which NAMD has been ported It should not be necessary for you to compile NAMD unless you wish to add or mod ify features or to improve performance by u
44. efficiency of PME For speed PMEGridSizeZ should have only small integer factors 2 3 and 5 PMEProcessors lt processors for FFT and reciprocal sum gt Acceptable Values positive integer Default Value larger of x and y grid sizes up to all available processors Description For best performance on some systems and machines it may be necessary to restrict the amount of parallelism used Experiment with this parameter if your parallel performance is poor when PME is used FFTWEstimate lt Use estimates to optimize FFT gt Acceptable Values yes or no Default Value no Description Do not optimize FFT based on measurements but on FF TW rules of thumb This reduces startup time but may affect performance FFTWUseWisdom lt Use FF TW wisdom archive file gt Acceptable Values yes or no Default Value yes Description Try to reduce startup time when possible by reading FFTW wisdom from a file and saving wisdom generated by performance measurements to the same file for future use This will reduce startup time when running the same size PME grid on the same number of processors as a previous run using the same file FFTWWisdomFile lt name of file for FFTW wisdom archive gt Acceptable Values file name Default Value FFTW_NAMD_version_platform txt 52 Description File where FFTW wisdom is read and saved If you only run on one platform this may be useful to reduce startup times for all runs The default is like
45. electrostatic interactions for pairs that are separated by less than the local interaction distance determined by the splitting function The long range component consists only of electrostatic interactions outside of the local interaction distance Since the long range forces are slowly varying they are not evaluated every timestep Instead they are evaluated every k timesteps specified by the NAMD parameter fullElectFrequency An impulse of k times the long range force is applied to the system every k timesteps i e the r RESPA integrator is used For appropriate values of k it is believed that the error introduced by this infrequent evaluation is modest compared to the error already incurred by the use of the numerical Verlet integrator Improved methods for incorporating these long range forces are currently being investigated with the intention of improving accuracy as well as reducing the frequency of long range force evaluations In the scheme described above the van der Waals forces are still truncated at the local interac tion distance Thus the van der Waals cutoff distance forms a lower limit to the local interaction distance While this is believed to be sufficient there are investigations underway to remove this limitation and provide full van der Waals calculations in O N time as well One of the areas of current research being studied using NAMD is the exploration of better methods for performing multiple timestep integration
46. from 0 to 1 while doubling stepspercycle and pairlistspercycle may help but it is important to benchmark The pairlist distance will adjust automatically and one pairlist per ten steps is a good ratio NAMD should scale very well when the number of patches multiply the dimensions of the patch grid is larger or rougly the same as the number of processors If this is not the case it may be possible to improve scaling by adding twoAwayX yes to the config file which roughly doubles the number of patches Similar options twoAwayY and twoAwayZ also exist and may be used in combination but this greatly increases the number of compute objects twoAwayX has the unique advantage of also improving the scalability of PME Additional performance tuning suggestions and options are described at http www ks uiuc edu Research namd wiki NamdPerformanceTuning 210 18 NAMD Availability and Installation NAMD is distributed freely for non profit use NAMD CV5S 2015 12 17 is based on the Charm messaging system and the Converse communication layer http charm cs uiuc edu which have been ported to a wide variety of parallel platforms This section describes how to obtain and install NAMD CVS 2015 12 17 18 1 How to obtain NAMD NAMD may be downloaded from http www ks uiuc edu Research namd You will be re quired to provide minimal registration information and agree to a license before receiving access to the software Both source and binary
47. group refPositionsFile lt File containing the reference positions for fitting gt Context atom group Acceptable Values UNIX filename Description Supplies the reference positions mutually exclusive with refPositions Atomic positions are read differently depending on the three following scenarios 4 refPositionsCol is specified the PDB file contains a set of position larger than the size of the group and positions are read according to the value of the column refPositionsCol which may be the same as atomsCol i refPositionsCol is not specified and the PDB file contains exactly as many ATOM records as the atoms in the group all positions are read in sequence iii refPositionsCol is not specified and the PDB file contains the entire system the positions corresponding to the numeric indices of the atom group are read refPositionsCol lt PDB column containing atom flags gt Context atom group Acceptable Values 0 B X Y or Z Description Like atomsCol for atomsFile indicates which column to use to identify the atoms in refPositionsFile refPositionsColValue lt Atom selection flag in the PDB column gt Context atom group Acceptable Values positive decimal Description Analogous to atomsColValue but applied to refPositionsCol refPositionsGroup lt Use an alternate set of atoms to define the roto translation gt Context atom group Acceptable Values Block refPositionsGroup Default Value This group
48. included in pairlist e NAMD Parameter 1 4scaling X PLOR Parameter E14Fac Scaling factor for 1 4 pair electrostatic interactions e NAMD Parameter dielectric X PLOR Parameter EPS Dielectric constant e NAMD Parameter exclude X PLOR Parameter NBXMod Both parameters specify which atom pairs to exclude from non bonded interactions The ability to ignore explicit exclusions is not present within NAMD thus only positive values of NBXMod have NAMD equivalents These equivalences are NBXMod 1 is equivalent to exclude none no atom pairs excluded NBXMod 2 is equivalent to exclude 1 2 only 1 2 pairs excluded NBXMod 3 is equivalent to exclude 1 3 1 2 and 1 3 pairs excluded NBXMod 4 is equivalent to exclude 1 4 1 2 1 3 and 1 4 pairs excluded NBXMod 5 is equivalent to exclude scaled1 4 1 2 and 1 3 pairs excluded 1 4 pairs modified 196 NAMD Parameter switching X PLOR Parameter SHIFt VSWItch and TRUNcation Activating the NAMD option switching is equivalent to using the X PLOR options SHIFt and VSWItch Deactivating switching is equivalent to using the X PLOR option TRUNcation NAMD Parameter temperature X PLOR Parameter FIRSttemp Initial temperature for the system NAMD Parameter rescaleFreq X PLOR Parameter IEQFrq Number of timesteps between velocity rescaling NAMD Parameter rescaleTemp X PLOR Parameter FINAltemp Temperature to which velocities are rescaled NAMD
49. instantaneous pres sure did not fluctuate randomly during a simulation and the compressibility estimate was exact then the inital pressure would decay exponentially to the target pressure with this time constant Having a longer relaxation time results in more averaging over pressure measure ments and hence smaller fluctuations in the cell volume A reasonable choice for relaxation time would be 100 fs The compressibility and the relaxation time appear only as a ratio in the dynamics so a larger compressibility is equivalent to a smaller relaxation time BerendsenPressureFreq lt how often to rescale positions gt Acceptable Values positive multiple of nonbondedFrequency and fullElectFrequency Default Value nonbondedFrequency or fullElectFrequency if used Description Specifies number of timesteps between position rescalings for Berendsen s method Primarily to deal with multiple timestepping integrators but also to reduce cell volume fluctuations cell rescalings can occur on a longer interval This could reasonably be between 1 and 20 timesteps but the relaxation time should be at least ten times larger 7 5 2 Nos Hoover Langevin piston pressure control NAMD provides constant pressure simulation using a modified Nos Hoover method in which Langevin dynamics is used to control fluctuations in the barostat This method should be combined with a method of temperature control such as Langevin dynamics in order to simulate the NPT ense
50. ion ti out alchOutFreq 5 alchEquilSteps 5000 alchVdWShiftCoeff 1 Enable soft core vdW potential alchElecLambdaStart 0 1 Introduce electrostatics for lambda gt 0 1 alchLambda 0 run 10000 alchLambda 0 00001 run 10000 alchLambda 0 0001 run 10000 alchLambda 0 001 run 10000 alchLambda 0 01 run 10000 set Lambda 0 1 while Lambda lt 0 9 4 alchLambda Lambda run 10000 set Lambda expr Lambda 0 1 alchLambda 0 99 run 10000 alchLambda 0 999 run 10000 alchLambda 0 9999 run 10000 alchLambda 0 99999 run 10000 alchLambda 1 run 10000 Robust sampling of the free energy of particle insertion is enabled by the use of soft core van der Waals scaling with the alchVdWShiftCoeff parameter delayed introduction of electrostatics with a non zero alchElecLambdaStart value and very gradual scaling of A towards its end points 172 11 4 Description of a free energy calculation output 11 4 1 Free Energy Perturbation When running FEP the alchOutFile contains electrostatic and van der Waals energy data calcu lated for alchLambda and alchLambda2 written every alchOutFreq steps The column dE is the energy difference of the single configuration dE_avg and dG are the instantaneous ensemble average of the energy and the calculated free energy at the time step specified in column 2 respectively The temperature is specified in the penultimate column Upon completion of alchEquilSteps steps the calculation of dE_avg a
51. is specified a new context is entered and the old context is returned If delete is also specified the old context is destroyed and deleted lt old context gt is returned An error is returned if the specified context does not exist or if delete was specified and the current context would still be in use It may be possible to write robust error tolerant code with this interface but it would not be easy Please employ the following revised psfcontext usage instead Arguments lt contert gt Context ID returned by psfcontext Context At any time psfcontext mixedcase Purpose Make context case sensitive by preserving case of all segment residue atom and patch names on input Arguments Context Before reading files requiring case sensitive behavior normally as the first com mand psfcontext allcaps Purpose Make context case insensitive by converting all segment residue atom and patch names to upper case characters on input This is the default behavior and should match the behavior of versions prior to 1 5 0 Arguments Context Before reading files requiring case insensitive behavior not needed in normal use psfcontext reset Purpose Clears the structure topology definitions and aliases creating clean environment just like a new context 42 Arguments Context At any time psfcontext create Purpose Creates a new context and returns its ID but does not switch to it This is different from psfcontext
52. is the potential energy function v can be interpreted as the direction along which the force acting on variable is measured whereas the second term in the average corresponds to the geometric entropy contribution that appears as a Jacobian correction in the classic formalism 15 Condition 51 states that the direction along which the system force on amp is measured is orthogonal to the gradient of which means that the force measured on does not act on Equation 52 implies that constraint forces are orthogonal to the directions along which the free energy gradient is measured so that the measurement is effectively performed on unconstrained degrees of freedom In NAMD constraints are typically applied to the lengths of bonds involving hydrogen atoms for example in TIP3P water molecules parameter rigidBonds section 5 6 1 In the framework of ABF F is accumulated in bins of finite size 6 thereby providing an estimate of the free energy gradient according to equation 50 The biasing force applied along the collective variables to overcome free energy barriers is calculated as 147 FAP a Ne x Ve A E 54 where Vz A denotes the current estimate of the free energy gradient at the current point in the collective variable subspace and a N is a scaling factor that is ramped from 0 to 1 as the local number of samples N increases to prevent nonequilibrium effects in the early phase of the simulation wh
53. itself Description If either centerReference or rotateReference is defined this keyword defines an alternate atom group to calculate the optimal roto translation Use this option to define a continuous rotation if the structure of the group involved changes significantly a typical symptom would be the message Warning discontinuous rotation The following example illustrates the syntax of refPositionsGroup a group called atoms is defined including 8 Ca atoms of a protein of 100 residues An optimal roto translation is calculated automatically by fitting the Ca trace of the rest of the protein onto the coordinates provided by a PDB file Example defining a group atoms with its coordinates expressed on a roto translated frame of reference defined by a second group atoms psfSegID PROT atomNameResidueRange CA 41 48 centerReference yes 128 rotateReference yes refPositionsGroup define the frame by fitting the rest of the protein psfSegID PROT PROT atomNameResidueRange CA 1 40 atomNameResidueRange CA 49 100 refPositionsFile all pdb can be the entire system The following two options have default values appropriate for the vast majority of applications and are only provided to support rare special cases e enableFitGradients lt Include the roto translational contribution to colvar gradients gt Context atom group Acceptable Values boolean Default Value on Description When either cen
54. key word 122 extForceFilename parameter 112 extForces parameter 112 extForcesCommand parameter 112 extraBonds parameter 64 extraBondsFile parameter 64 colvar FFTWEstimate parameter 52 FFTWUseWisdom parameter 52 FFTWWisdomFile parameter 52 first psfgen command 40 firsttimestep parameter 77 fixedAtoms parameter 17 63 fixedAtomsCol parameter 64 fixedAtomsFile parameter 64 fixedAtomsForces parameter 17 63 221 forceConstant colvars harmonic keyword 157 forceConstant colvars linear keyword 161 forceDCDfile parameter 26 forceDCDfreq parameter 26 forceNoPBC colvars distanceZ distanceXY keyword 132 forceNoPBC colvars distance keyword 131 forceRange colvars alb keyword 162 FullDirect parameter 56 fullElectFrequency parameter 78 fullSamples colvars abf keyword 149 GBIS parameter 70 GBISBeta parameter 70 GBISDelta parameter 70 GBISGamma parameter 70 GoCoordinates parameter 188 GoForcesOn parameter 187 GoMethod parameter 188 GoParameters parameter 187 GPRESSAVG 27 GPRESSURE 27 grocoorfile parameter 30 190 gromacs parameter 30 189 GromacsPair parameter 190 grotopfile parameter 30 189 groupl colvars distance keyword 131 group2 colvars distance keyword 131 group2CenterOnly colvars coordNum keyword 135 guesscoord psfgen command 44 hardLowerBoundary colvars colvar keyword 119 hardUpperBoundary colvars colvar keyword 120 hBondCoeff colvars alpha k
55. model the ordering of atoms within each TIP4P water molecule must be oxygen hydrogen hydrogen lone pair When using the SWM4 NDP water model the ordering of atoms within each SWM4 NDP water molecule must be oxygen Drude particle lone pair hydrogen hydrogen Alternative orderings will fail 5 4 Drude polarizable force field The Drude oscillator model represents induced electronic polarization by introducing an auxiliary particle attached to each polarizable atom via a harmonic spring The advantage with the Drude model is that it preserves the simple particle particle Coulomb electrostatic interaction employed in nonpolarizable force fields thus its implementation in NAMD is more straightforward than alter native models for polarization NAMD performs the integration of Drude oscillators by employing a novel dual Langevin thermostat to freeze the Drude oscillators while maintaining the warm de grees of freedom at the desired temperature 38 Use of the Langevin thermostat enables better parallel scalability than the earlier reported implementation which made use of a dual Nos Hoover thermostat acting on and within each nucleus Drude pair 45 Performance results show that the NAMD implementation of the Drude model maintains good parallel scalability with an increase in computational cost by not more than twice that of using a nonpolarizable force field 38 The Drude polarizable force field requires some extensions to the CHARMM force
56. namd2 local p lt procs gt lt configfile gt You may need to specify the full path to the namd2 binary 17 2 Windows Clusters and Workstation Networks The Win64 MPI version of NAMD runs on Windows HPC Server and should be launched as you would any other MPI program 17 3 Linux Clusters with InfiniBand or Other High Performance Networks Charm provides a special ibverbs network layer that uses InfiniBand networks directly through the OpenFabrics OFED ibverbs library This avoids efficiency and portability issues associated with MPI Look for pre built ibverbs NAMD binaries or specify ibverbs when building Charm Writing batch job scripts to run charmrun in a queueing system can be challenging Since most clusters provide directions for using mpiexec to launch MPI jobs charmrun provides a mpiexec option to use mpiexec to launch non MPI binaries If mpiexec np procs is not sufficient to launch jobs on your cluster you will need to write an executable mympiexec script like the following from TACC 203 bin csh shift shift exec ibrun x The job is then launched with full paths where needed as charmrun p lt procs gt mpiexec remote shell mympiexec namd2 lt configfile gt For workstation clusters and other massively parallel machines with special high performance networking NAMD uses the system provided MPI library with a few exceptions and standard system tools such as mpirun are used to launch jobs Sinc
57. new above which switches to the newly created context and returns the current context s ID Arguments Context At any time psfcontext delete lt contert gt Purpose Deletes the specified context An error is returned if the specified context does not exist or would still be in use This is different from psfcontext lt context gt delete above which switches to the specified context and deletes the current one Arguments lt contert gt Context ID returned by psfcontext Context At any time psfcontext eval lt context gt lt commands gt y Purpose Evaluates lt commands gt in the specified context returning to the current context on exit This should be totally robust returning to the orignal context in case of errors and preventing its deletion when nested Arguments lt contert gt Context ID returned by psfcontext create lt commands gt Script to be executed in the specified context Context At any time psfcontext stats Purpose Returns the total numbers of contexts that have been created and destroyed This is useful for checking if a script is leaking contexts Arguments Context At any time writepsf charmm x plor cmap nocmap lt file name gt Purpose Write out structure information as PSF file A simplified session log is listed in the REMARKS section of the PSF file Arguments charmm Use CHARMM format numbers for atom types x plor Use X PLOR format names for atom types the de
58. not an arbitrary selection The coordinates for the target structure are also taken from the targeted atoms in this file Non targeted atoms are ignored The beta column of targetted atoms is used to designate non overlapping constraint domains Forces will be calculated for atoms within a domain separately from atoms of other domains TMDFirstStep lt first TMD timestep gt Acceptable Values Positive integer Default Value 0 Description TMDLastStep lt last TMD timestep gt Acceptable Values Positive integer Description TMD forces are applied only between TMDFirstStep and TMDLastStep The target RMSD evolves linearly in time from the initial to the final target value TMDInitialRMSD lt target RMSD at first TMD step gt Acceptable Values Non negative value in A Default Value from coordinates Description In order to perform TMD calculations that involve restarting a previous NAMD run be sure to specify TMDInitialRMSD with the same value in each NAMD input file and use the NAMD parameter firstTimestep in the continuation runs so that the target RMSD continues from where the last run left off TMDFinalRMSD lt target RMSD at last TMD step gt Acceptable Values Non negative value in A Default Value 0 Description If no TMDInitialRMSD is given the initial RMSD will be calculated at the first TMD step TMDFinalRMSD may be less than or greater than TMDInitialRMSD depending on whether the system is to be steered toward
59. of atoms The block gyration defines the pa rameters for calculating the radius of gyration of a group of atomic positions x1 t x2 t xy t with respect to their center of geometry Xcog t pe Reyr F N x t Xcog t 41 i 1 This component must contain one atoms block to define the atom group and returns a positive number expressed in inertia total moment of inertia of a group of atoms The block inertia de fines the parameters for calculating the total moment of inertia of a group of atomic positions x1 t x2 t xn t with respect to their center of geometry Xcog t N 1 Y xi t Xcoglt l 42 i l Note that all atomic masses are set to 1 for simplicity This component must contain one atoms block to define the atom group and returns a positive number expressed in A inertiaZ total moment of inertia of a group of atoms around a chosen axis The block inertiaZ defines the parameters for calculating the component along the axis e of the moment of inertia of a group of atomic positions x1 t xa t xw t with respect to their center of geometry Xcog t N To Y xilt Xcog 43 i l Note that all atomic masses are set to 1 for simplicity This component must contain one atoms block to define the atom group and returns a positive number expressed in Ae The following option may also be provided e axis lt Projection axis A gt Co
60. of the configuration file The complete list of selection keywords available in NAMD is e atomNumbers lt List of atom numbers gt Context atom group 125 Acceptable Values space separated list of positive integers Description This option adds to the group all the atoms whose numbers are in the list The number of the first atom in the system is 1 to convert from a VMD selection use atomselect get serial indexGroup lt Name of index group to be used GROMACS format gt Context atom group Acceptable Values string Description If the name of an index file has been provided by indexFile this option allows to select one index group from that file the atoms from that index group will be used to define the current group atomNumbersRange lt Atoms within a number range gt Context atom group Acceptable Values lt Starting number gt lt Ending number gt Description This option includes in the group all atoms whose numbers are within the range specified The number of the first atom in the system is 1 atomNameResidueRange lt Named atoms within a range of residue numbers gt Context atom group Acceptable Values lt Atom name gt lt Starting residue gt lt Ending residue gt Description This option adds to the group all the atoms with the provided name within residues in the given range psfSegID lt PSF segment identifier gt Context atom group Acceptable Values space separated list of stri
61. of the interpolant MSMApprox lt select the interpolant gt Acceptable Values 0 1 7 Default Value 0 Description Select the interpolation scheme 0 sets C cubic p 3 interpolation 1 sets C quintic p 5 interpolation 2 sets C quintic p 5 interpolation 3 sets C septic p 7 interpolation 4 sets C septic p 7 interpolation 54 5 sets C nonic interpolation p 9 6 sets Ct nonic p 9 interpolation 7 sets C1 Hermite p 4 interpolation MSMSplit lt select the splitting gt Acceptable Values 0 1 6 Default Value 0 Description Select the splitting function 0 sets C Taylor splitting 1 sets C Taylor splitting 2 sets Ct Taylor splitting 3 sets C Taylor splitting 4 sets C Taylor splitting 5 sets C Taylor splitting 6 sets C Taylor splitting MSMLevels lt maximum number of levels gt Acceptable Values non negative integer Default Value 0 Description Set the maximum number of levels to use in the grid hierarchy Although setting slightly lower than the default might or might not improve performance and or accuracy for non periodic simulation it is generally best to leave this at the default value 0 which will then automatically adjust the levels to the size of the given system MSMPadding lt grid padding A gt Acceptable Values non negative real Default Value 2 5 Description
62. on symmetryFirstFullStep and symmetryLastFullStep e symmetryFile lt File for symmetry information gt Acceptable Values Path to PDB file Description Restrained atoms are those whose occupancy O is nonzero in the symmetry pdb file The file must contain no more atoms than the structure file and those atoms present must have the exact same index as the structure file i e the file may contain a truncated atom selection index lt N but not an arbitrary selection The value in the occupancy column represent the symmetry group the atom belongs to These symmetry groups are used for denoting monomers of the same type These groups will be transformed by the matrices in their own symmetryMatrixFile and averaged separetely from other groups The designation in the occupancy column should be an integer value starting at 1 and proceeding in ascending order mirroring the order of the corresponding matrix file within the configuration file e g the first symmetryMatrixFile contains the matrices for symmetry group 1 The value in the atom s beta column represents its monomer designation This should be an integer value starting at 1 and proceeding in ascending order relative to the order of the corresponding transformation matrix found in the symmetry group s symmetryMatrixFile If an atom is contained in more than one symmetry group additional pdb files can be listed These pdb files should follow the same rules as the first one un
63. one non negative value for each colvar The unit of force is kcal mol divided by the colvar unit e hideJacobian lt Remove geometric entropy term from calculated free energy gradient gt Context abf Acceptable Values boolean Default Value no Description In a few special cases most notably distance based variables an alternate definition of the potential of mean force is traditionally used which excludes the Jacobian term describing the effect of geometric entropy on the distribution of the variable This results for example in particle particle potentials of mean force being flat at large separations Setting this parameter to yes causes the output data to follow that convention by removing this contribution from the output gradients while applying internally the corresponding correction to ensure uniform sampling It is not allowed for colvars with multiple components e outputFreq lt Frequency in timesteps at which ABF data files are refreshed gt Context abf Acceptable Values positive integer Default Value Colvar module restart frequency Description The files containing the free energy gradient estimate and sampling histogram and the PMF in one dimensional calculations are written on disk at the given time interval 149 e historyFreq lt Frequency in timesteps at which ABF history files are accumulated gt Context abf Acceptable Values positive integer Default Value 0 Description If this number is non zero
64. option applies only to extended Lagrangian colvars If colvarsTrajFrequency is defined the kinetic energy of the extended degree and freedom and the potential energy of the restraining spring are are written to the trajectory file under the labels Ek_ lt name gt and Ep_ lt name gt outputSystemForce lt Output a system force trajectory for this colvar gt Context colvar Acceptable Values boolean Default Value off Description If colvarsTrajFrequency is defined the total system force on this colvar i e the projection of all interatomic forces except constraint forces on this colvar see equation 53 in section 10 5 1 are written to the trajectory file under the label fs_ lt name gt For extended Lagrangian colvars the system force felt by the extended degree of freedom is simply the force from the harmonic spring Note not all components support this option The physical unit for this force is kcal mol divided by the colvar unit U outputAppliedForce lt Output an applied force trajectory for this colvar gt Context colvar Acceptable Values boolean Default Value off 121 Description If colvarsTrajFrequency is defined the total force applied on this colvar by biases and confining potentials walls within the colvar module are written to the trajectory under the label fa_ lt name gt For extended Lagrangian colvars this force is actually applied to the extended degree of freedom rathe
65. param value as well as param value This is supported but only before the first run command For an easy life use param value 18 2 2 3 Multiple copy replica exchange scripting interface Multiple copy or replica based algorithms are supported by the following commands which utilize two sided semantics modeled on MPI e myReplica e numReplicas e replicaBarrier e replicaSend data dest e replicaRecv source e replicaSendrecv data dest source e replicaAtomSend dest e replicaAtomRecv source e replicaAtomSendrecv dest source The replicaSend Sendrecv data argument may be any string and hence any Tcl object e g a list that can be represented as a string Data received from the source replica is returned by replicaRecv Sendrecv In order to ensure message ordering replicaSend Sendrecv will block until the corresponding remote receive call except when replicaSend is called from inside replicaEval as discussed below The parameter replicaUniformPatchGrids must be true for atom exchange replicaAtom or remote checkpointing checkpoint with a second argument see below The following additional commands utilize one sided semantics and should provide a complete feature set for running a simulation with fewer NAMD replica partitions than logical replicas e checkpointStore key replica or global e checkpointLoad key replica or global e checkpointSwap key replica or global e checkpointFree ke
66. periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellBasisVector2 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellBasisVector3 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellOrigin lt center of periodic cell A gt Acceptable Values position Default Value 000 Description When position rescaling is used to control pressure this location will remain constant Also used as the center of the cell for wrapped output coordinates e extendedSystem lt XSC file to read cell parameters from gt Acceptable Values file name Description In addition to coor and vel output files NAMD generates a xsc eXtended System Configuration file which contains the periodic cell parameters and extended system variables such as the strain rate in constant pressure simulations Periodic cell parameters will be read from this file if this option is present ignoring the above parameters e XSTfile lt XST file to write cell trajectory to gt Acceptable Values file name Default Value outputname xst Description _NAMD can also generate a xst eXtended System Trajectory file which contains a record of
67. potential in the aMDT mode In the dual boost mode aMDdual 29 two independent boost energies are applied one on the dihedral potential and the other on the Total Dihedral 4 65 potential 175 Figure 11 Schematics of the aMD method When the original potential thick line falls below a threshold energy E dashed line a boost potential is added The modified energy profiles thin lines have smaller barriers separating adjacent energy basins 12 1 2 NAMD parameters The following parameters are used to enable accelerated MD e accelMD lt Is accelerated molecular dynamics active gt Acceptable Values on or off Default Value off Description Specifies if accelerated MD is active e accelMDdihe lt Apply boost to dihedrals gt Acceptable Values on or off Default Value on Description Only applies boost to the dihedral potential By default accelMDdihe is turned on and the boost energy is applied to the dihedral potential of the simulated system When accelMDdihe is turned off aMD switches to the accelMDT mode and the boost is applied to the total potential e accelMDE lt Threshold energy E gt Acceptable Values Real number Description Specifies the threshold energy E in the aMD equations e accelMDalpha lt Acceleration factor a gt Acceptable Values Positive real number Description Specifies the acceleration factor a in the aMD equations e accelMDdual lt Use dual boo
68. qi q2 q3 quadruplet Default Value 1 0 0 0 0 0 0 0 null rotation Description Between the two equivalent quaternions qo q1 q2 q3 and d0 41 q2 q3 the closer to 1 0 0 0 0 0 0 0 is chosen This simplifies the visualization of the colvar trajectory when samples values are a smaller subset of all possible rotations Note this only affects the output never the dynamics Hint stopping the rotation of a protein To stop the rotation of an elongated macro molecule in solution and use an anisotropic box to save water molecules it is possible to define a colvar with an orientation component and restrain it throuh the harmonic bias around the identity rotation 1 0 0 0 0 0 0 0 Only the overall orientation of the macromolecule is affected and not its internal degrees of freedom The user should also take care that the macro molecule is composed by a single chain or disable wrapA11 otherwise orientationAngle angle of rotation from reference coordinates The block orientationAngle accepts the same base options as the component orientation atoms and refPositions or refPositionsFile refPositionsCol and refPositionsColValue The returned value is the angle of rotation 0 between the current and the reference positions This angle is expressed in degrees within the range 0 180 orientationProj cosine of the angle of rotation from reference coordinates The block orientationProj accepts t
69. representative of the initial reference state a a e X a X b X c Figure 8 Convergence of an FEP calculation If the ensembles representative of states a and b are too disparate equation 59 will not converge a If in sharp contrast the configurations of state b form a subset of the ensemble of configurations characteristic of state a the simulation is expected to converge b The difficulties reflected in case a may be alleviated by the introduction of mutually overlapping intermediate states that connect a to b c It should be mentioned that in practice the kinetic contribution 7 Pz is assumed to be identical for state a and state b Convergence of equation 59 implies that low energy configurations of the target state b are also configurations of the reference state a thus resulting in an appropriate overlap of the corresponding ensembles see Figure 8 Transformation between the two thermodynamic states is replaced by a series of transformations between non physical intermediate states along a well delineated pathway that connects a to b This pathway is characterized by the general extent parameter 8 39 40 48 A that makes the Hamiltonian and hence the free energy a continuous function of this parameter between a and b N Also 3 In exp 8 Mbs Pas Ait MOS Pai A 60 i 1 Here N stands for the number of intermediate stages or windows betw
70. segment residue and name For example atomid br 2 N e addatom lt atomid gt Request coordinates of this atom for next force evaluation and the calculated total force on this atom for current force evaluation Request remains in effect until clearconfig is called For example addatom 4 or addatom atomid br 2 N e addgroup lt atomid list gt Request center of mass coordinates of this group for next force evaluation Returns a group ID which is of the form gN where N is a small integer This group ID may then be used to find coordinates and apply forces just like a regular atom ID Aggregate forces may then be applied to the group as whole Request remains in effect until clearconfig is called For example set groupid addgroup 14 10 12 e clearconfig Clears the current list of requested atoms After clearconfig calls to addatom and addgroup can be used to build a new configuration e getstep Returns the current step number e loadcoords lt varname gt Loads requested atom and group coordinates in A into a local array loadcoords should only be called from within the calcforces procedure For example loadcoords p and print p 4 e loadforces lt varname gt Loads the forces applied in the previous timestep in kcal mol T into a local array loadforces should only be called from within the calcforces procedure For example loadforces f and print f 4 e enableto
71. simulation e adaptTempBins lt number of temperature bins gt Acceptable Values Positive integer Default Value 1000 Description Sets the number of bins to subdivide the temperature range Each bin stores the average energy for the given temperature e adaptTempDt lt stepsize for temperature updates gt Acceptable Values Positive real numbers Default Value 107 Description Integration timestep for temperature updates This is unrelated to the simulation timestep and only scales the size of the step taken in temperature space every adaptTempFreq steps e adaptTempInFile lt adaptive tempering input filename gt Acceptable Values UNIX filename Description The input file containing restart information for adaptive tempering written out by adaptTempRestartFile 178 adaptTempRestartFile lt adaptive tempering restart filename gt Acceptable Values UNIX filename Description The file to write out restart information for adaptive tempering adaptTempRestartFreq lt steps between writing restart file gt Acceptable Values Positive integer Description Frequency of writing restart file adaptTempLangevin lt send temperature updates to langevin thermostat gt Acceptable Values on or off Default Value on Description Setting this to on will cause the langevin thermostat to use the updated tem peratures from adaptive tempering Note that either one of adaptTempLangevin or adapt TempRescaling have to be on ada
72. systems The method replaces the physical based nonbonded interactions with a smoother knowledge based potential energy surface Bonded interactions are taken from the classical force fields By removing energetic traps along a MD trajectory the system will be able to sample states not normally accessible to classical MD simulations 13 1 2 Hybrid MD Go considerations Typically Go simulations are conducted in the absence of solvent and with electrostatic and van der Waals forces in the system turned off to improve conformational space exploration Due to the current implementation of Go the partial charges and van der Waals radii need to be set to zero in the psf and parameter file to remove the physical nonbonded interactions Additionally NAMD uses a reference PDB structure to construct the Go pairwise potential between atoms Finally the Go model in NAMD introduces the idea of chain types Consider modeling a protein nucleic acid complex Using classical all atom MD a single force field describes all possible nonbonded interactions With Go however one can create separate nonbonded force fields to describe the protein and nucleic acid interactions In order to create separate force fields atoms are grouped together using chain types where the chain types are taken from the occupancy field of the reference PDB file For argument sake assume that the protein atoms have an occupancy value of 1 0 and that the nucleic acid atoms have an occupan
73. target pressure bar gt Acceptable Values positive decimal Description Specifies target pressure for Langevin piston method A typical value would be 1 01325 bar atmospheric pressure at sea level e LangevinPistonPeriod lt oscillation period fs gt Acceptable Values positive decimal Description Specifies barostat oscillation time scale for Langevin piston method If the instantaneous pressure did not fluctuate randomly during a simulation and the decay time was infinite no friction then the cell volume would oscillate with this angular period Having a longer period results in more averaging over pressure measurements and hence slower fluctuations in the cell volume A reasonable choice for the piston period would be 200 fs e LangevinPistonDecay lt damping time scale fs gt Acceptable Values positive decimal Description Specifies barostat damping time scale for Langevin piston method A value larger than the piston period would result in underdamped dynamics decaying ringing in the cell volume while a smaller value approaches exponential decay as in Berendsen s method above A smaller value also corresponds to larger random forces with increased coupling to the Langevin temperature bath Typically this would be chosen equal to or smaller than the piston period such as 100 fs 86 LangevinPistonTemp lt noise temperature K gt Acceptable Values positive decimal Description Specifies barostat noise temperature
74. the edge of the grid with the values of the corresponding edge of the periodic image of the grid The current size of the simulation box is taken into account so that as the simulation box size fluctuates the force on an atom outside of the grid varies continuously until it re enters the opposite edge of the grid If the grid is not continuous in this direction the interpolated force on atoms near the edge of the grid is calculated so that it continuously approaches zero as an atom approaches the edge of the grid e mgridforcecont2 lt tag gt lt ls grid continuous in the direction of the second basis vector gt Acceptable Values yes or no Default Value no Description Operates the same as mgridforcecont1 except applies in the direction of the second basis vector e mgridforcecont3 lt tag gt lt Is grid continuous in the direction of the third basis vector gt Acceptable Values yes or no Default Value no Description Operates the same as mgridforcecont1 except applies in the direction of the third basis vector e mgridforcevoff lt tag gt lt Offset periodic images of the grid by specified amounts gt Acceptable Values vector of decimals x y z Default Value 00 0 Description If a continuous grid is used along a particular basis vector it may be desirable to shift the potentials in the image to manipulate the potential outside the grid For example consider the case where the potential is a ramp in the x direction and
75. the extended degree of freedom undergoes Langevin dy namics at temperature extendedTemp The friction force is minus extendedLangevinDamping times the velocity This is useful because the extended dynamics coordinate may heat up in the transient non equilibrium regime of ABF Use moderate damping values to limit viscous friction potentially slowing down diffusive sampling and stochastic noise increasing the variance of statistical measurements In doubt use the default value 10 2 5 Statistical analysis of collective variables When the global keyword analysis is defined in the configuration file run time calculations of statistical properties for individual colvars can be performed At the moment several types of time correlation functions running averages and running standard deviations are available e corrFunc lt Calculate a time correlation function gt Context colvar Acceptable Values boolean Default Value off Description Whether or not a time correlaction function should be calculated for this colvar e corrFuncWithColvar lt Colvar name for the correlation function gt Context colvar Acceptable Values string Description By default the auto correlation function ACF of this colvar amp is cal culated When this option is specified the correlation function is calculated instead with another colvar j which must be of the same type scalar vector or quaternion as e corrFuncType lt Type of the co
76. the periodic cell parameters and extended system variables during the simulation If XSTfile is defined then XSTfreq must also be defined e XSTfreq lt how often to append state to XST file gt Acceptable Values positive integer 72 Description Like the DCDfreq option controls how often the extended system configura tion will be appended to the XST file e wrapWater lt wrap water coordinates around periodic boundaries gt Acceptable Values on or off Default Value off Description Coordinates are normally output relative to the way they were read in Hence if part of a molecule crosses a periodic boundary it is not translated to the other side of the cell on output This option alters this behavior for water molecules only e wrapAll lt wrap all coordinates around periodic boundaries gt Acceptable Values on or off Default Value off Description Coordinates are normally output relative to the way they were read in Hence if part of a molecule crosses a periodic boundary it is not translated to the other side of the cell on output This option alters this behavior for all contiguous clusters of bonded atoms e wrapNearest lt use nearest image to cell origin when wrapping coordinates gt Acceptable Values on or off Default Value off Description Coordinates are normally wrapped to the diagonal unit cell centered on the origin This option combined with wrapWater or wrapA11 wraps coordinates to the nearest image t
77. the system force is measured along a vector field see equation 53 in section 10 5 1 that only involves atoms of group1 See section 10 5 1 for an example coordNum coordination number between two groups The coordNum block defines a coordination number or number of contacts which calculates the function 1 d do 1 d do where dy is the cutoff distance and n and m are exponents that can control its long range behavior and stiffness 37 This function is summed over all pairs of atoms in group1 and group2 s 1 xi xj do C groupi group2 af group1 group2 ma aoe 1 x xj do 37 groupi j Egroup2 This colvar component accepts the same keywords as the component distance group1 and group2 In addition to them it recognizes the following keywords e cutoff lt Interaction distance A gt Context coordNum 134 Acceptable Values positive decimal Default Value 4 0 Description This number defines the switching distance to define an interatomic contact for d lt do the switching function 1 d do 1 d do is close to 1 at d do it has a value of n m 1 2 with the default n and m and at d gt dp it goes to zero approximately like d Hence for a proper behavior m must be larger than n e cutoff3 lt Reference distance vector A gt Context coordNum Acceptable Values x y z triplet of positive decimals Defa
78. then a filename of outfile would be modified to scr outfile while a filename of tmp outfile would remain unchanged If no value for cwd is specified than all filenames are left unchanged but are assumed to be relative to the directory which contains the configuration file given on the command line 3 2 2 Output files e outputname lt output file prefix gt Acceptable Values UNIX filename prefix Description At the end of every simulation NAMD writes two files one containing the final coordinates and another containing the final velocities of all atoms in the simulation This option specifies the file prefix for these two files as well as the default prefix for trajectory and restart files The position coordinates will be saved to a file named as this prefix with coor 24 appended The velocities will be saved to a file named as this prefix with vel appended For example if the prefix specified using this option was tmp output then the two files would be tmp output coor and tmp output vel binaryoutput lt use binary output files gt Acceptable Values yes or no Default Value yes Description Enables the use of binary output files If this option is not set to no then the final output files will be written in binary rather than PDB format Binary files preserve more accuracy between NAMD restarts than ASCII PDB files but the binary files are not guaranteed to be transportable between computer architectures The atom coun
79. thermodynamics of mutant proteins A molecular dynamics analysis Science 244 1069 1072 1989 M K Gilson J A Given B L Bush and J A McCammon The statistical thermodynamic basis for computation of binding affinities A critical review Biophys J 72 1047 1069 1997 N M Glykos Carma a molecular dynamics analysis program J Comput Chem 27 14 1765 1768 2006 H Grubmiiller Predicting slow structural transitions in macromolecular systems Conforma tional flooding Phys Rev E 52 3 2893 2906 Sep 1995 D Hamelberg C de Oliveira and J McCammon Sampling of slow diffusive conformational transitions with accelerated molecular dynamics J Chem Phys 127 155102 2007 D Hamelberg J Mongan and J McCammon Accelerated molecular dynamics a promising and efficient simulation method for biomolecules J Chem Phys 120 24 11919 11929 2004 E Harder V M Anisimov I V Vorobyov P E M Lopes S Y Noskov A D MacKerell and B Roux Atomic level anisotropy in the electrostatic modeling of lone pairs for a polarizable force field based on the classical drude oscillator J Chem Theor Comp 2 6 1587 1597 2006 D J Hardy Z Wu J C Phillips J E Stone R D Skeel and K Schulten Multilevel summation method for electrostatic force evaluation J Chem Theor Comp 11 766 779 2015 214 33 40 41 42 43 44 45 46 47 G D Hawkins C J Cramer a
80. time in number of steps of the time correlation function default t 0 Note the value at t 0 is always used for the normalization corrFuncOutputFile lt Output file for the time correlation function gt Context colvar Acceptable Values UNIX filename Default Value lt name gt corrfunc dat Description The time correlation function is saved in this file runAve lt Calculate the running average and standard deviation gt Context colvar Acceptable Values boolean Default Value off Description Whether or not the running average and standard deviation should be cal culated for this colvar runAveLength lt Length of the running average window gt Context colvar Acceptable Values positive integer Default Value 1000 Description Length in number of points of the running average window runAveStride lt Stride of the running average window values gt Context colvar Acceptable Values positive integer Default Value 1 Description Number of steps between two values within the running average window runAveQutputFile lt Output file for the running average and standard deviation gt Context colvar 124 Acceptable Values UNIX filename Default Value lt name gt runave dat Description The running average and standard deviation are saved in this file 10 3 Selecting atoms for colvars defining atom groups 10 3 1 Selection keywords To define collective variables atoms are usually selected
81. time exploring values that are too large A value of 3 kT has worked well in the systems presented as a first choice This parameter is dynamically adjusted over the course of a simulation The benefit is that a bad guess for the forceRange can be corrected However this can lead to large amounts of energy being added over time to the system To prevent this dynamic update add hardForceRange yes as a parameter e rateMax lt The maximum rate of change of force constant gt Context alb Acceptable Values A list of space separated real numbers Description This optional parameter controls how much energy is added to the system from this bias Tuning this separately from the updateFrequency and forceRange can allow for large bias changes but with a low rateMax prevents large energy changes that can lead to instability in the simulation 10 5 6 Multidimensional histograms The histogram feature is used to record the distribution of a set of collective variables in the form of a N dimensional histogram It functions as a collective variable bias and is invoked by adding a histogram block to the colvars configuration file In addition to the common parameters name and colvars described above a histogram block may define the following parameter e outputFreq lt Frequency in timesteps at which the histogram file is refreshed gt Context histogram Acceptable Values positive integer Default Value Colvar module restart frequency 162
82. total GB energy with respect to relative atom distances rij po _ gt Ei 8 g gt 2 J where the partial derivatives are included since the Born radius a is a function of all relative atom distances The total GB energy of the system is DR E 11 2 i j gt i EFP d k E 2 Oar dry Ori OnG da OESB do DEF 0a drij l da drij Ori fji 9 Pi 10 where ESP is the Born radius dependent self energy of atom i and the GB energy between atoms i and j is given by l P PD i 12 fij The dielectric term 67 is 1 P Du exp rta 13 Ep Es and the GB function 68 is r2 2 Fij ri 0505 exp e 14 As the Born radii of atoms i and j decrease increasing screening the effective distance between the atoms fij increases The implicit solvent implemented in NAMD is the model of Onufriev Bashford and Case 55 56 which calculates the Born radius as 1 Qk A tanh dv By vo 15 PkO where Uk Pko ye Hy 16 i Hj is the piecewise descreening function 56 33 62 the seven piecewise regimes are O Tij gt Pret Pjs sphere j beyond cutoff I rij gt Te Pjs sphere j partially within cutoff Il rij gt 4pjs artificial regime for smoothing Regimes 4 III rij gt pio pjs spheres not overlapping 17 IV rij gt pio pjs spheres overlapping V pio lt Pjs sphere i inside sphere j VI otherwise sphere j inside sphere j 67
83. useGrids colvars metadynamics keyword 154 useGroupPressure parameter 17 84 useSettle parameter 62 vdwForceSwitching parameter 49 vdwGeometricSigma parameter 50 vector colvars eigenvector keyword 138 vectorCol colvars eigenvector keyword 138 vectorColValue colvars eigenvector key word 138 vectorFile colvars dihedralPC keyword 143 vectorFile colvars eigenvector keyword 138 vectorNumber colvars dihedralPC keyword 143 velDCDfile parameter 26 velDCDfreq parameter 26 velocities parameter 24 velocityQuenching parameter 76 waterModel parameter 58 wellTempered colvars metadynamics key word 155 width colvars colvar keyword 119 wrapAll parameter 73 226 wrapAround colvars distanceZ dihedral or spinAngle keyword 144 wrapNearest parameter 73 wrapWater parameter 73 writeFreeEnergyFile colvars metadynamics keyword 153 writeHillsTrajectory colvars metadynamics keyword 157 writenamdbin psfgen command 45 writepdb psfgen command 44 writepsf psfgen command 43 XSTfile parameter 72 XSTfreq parameter 72 zeroMomentum parameter 78
84. with O N terms in the summation The nonbonded potential terms involve interactions between all pairs of atoms usually excluding pairs of atoms already involved in a bonded term with O N terms in the summation although fast evaluation techniques are used to compute good approximations to their contribution to the potential with O N or O N log N computational cost 5 1 1 Bonded potential energy terms The bonded potential terms involve 2 3 and 4 body interactions of covalently bonded atoms The 2 body spring bond potential describes the harmonic vibrational motion between an i 7 pair of covalently bonded atoms Ubond k rij ro 3 where ri 17 m gives the distance between the atoms ro is the equilibrium distance and k is the spring constant The 3 body angular bond potential describes the angular vibrational motion occurring between an i j k triple of covalently bonded atoms Uangle ko 0 a 6 F kub Tik Tub 4 where in the first term 0 is the angle in radians between vectors fij rj T and fki Tj Tk Oo is the equilibrium angle and kg is the angle constant The second term is the Urey Bradley term used to describe a noncovalent spring between the outer and k atoms active when constant kub 0 where like the spring bond rik IF 7 gives the distance between the pair of atoms and rup is the equilibrium distance The 4 body torsion angle also known as dihedr
85. 0 833333 1 1 2 default is 1 0 3 4 GROMACS force field parameters NAMD has the ability to load GROMACS ASCII topology top and coordinate gro files which allows you to run most GROMACS simulations in NAMD All simulation output will still be in the traditional NAMD formats e gromacs lt use GROMACS format force field gt Acceptable Values on or off Default Value off Description If gromacs is set to on then grotopfile must be defined and structure and parameters should not be defined e grotopfile lt GROMACS format topology parameter file gt Acceptable Values UNIX filename Description This file contains complete topology and parameter information of the system e grocoorfile lt GROMACS format coordinate file gt Acceptable Values UNIX filename Description This file contains the coordinates of all the atoms Note that coordinates 30 can also be used for PDB format coordinate file When gromacs is set to on either grocoorfile or coordinates must be defined but not both However NAMD does not have support for many GROMACS specific options e Dummies fake atoms with positions generated from the positions of real atoms are not supported e The GROMACS pairs section where explicit 1 4 parameters are given between pairs of atoms is not supported since NAMD calculates its 1 4 interactions exclusively by type e Similarly exclusions are not supported The biggest problem here is that GROMAC
86. 01 Description This option sets the height W of the hills that are added during this run Lower values provide more accurate sampling at the price of longer simulation times to com plete a PMF calculation e newHillFrequency lt Frequency of hill creation gt Context metadynamics Acceptable Values positive integer Default Value 1000 Description This option sets the number of integration steps after which a new hill is added to the metadynamics potential Its value determines the parameter t in eq 55 Higher values provide more accurate sampling at the price of longer simulation times to complete a PMF calculation It is the user s responsibility to either leave hillWeight and newHillFrequency at their default values or to change them to match the specifics of each system The parameter g is instead defined as approximately half the width of the corresponding colvar amp see 10 2 1 Output files When interpolating grids are enabled default behavior the PMF is written every colvarsRestartFrequency steps to the file outputName pmf The following two options allow to control this behavior and to visually track statistical convergence e writeFreeEnergyFile lt Periodically write the PMF for visualization gt Context metadynamics 153 Acceptable Values boolean Default Value on Description When useGrids and this option are on the PMF is written every colvarsRestartFrequency steps e saveFreeEnergyFile lt Keep a
87. 09 e nearest the equivalent position nearest to the cell0rigin The following commands are available from within the calcforces procedure e nextatom Sets the internal counter to a new atom and return 1 or return 0 if all atoms have been processed this may even happen the first call This should be called as the condition of a while loop i e while mextatom 4 to iterate over all atoms One one atom may be accessed at a time e dropatom Excludes the current atom from future iterations on this processor until cleardrops is called Use this to eliminate extra work when an atom will not be needed for future force calculations If the atom migrates to another processor it may reappear so this call should be used only as an optimization e cleardrops All available atoms will be iterated over by nextatom as if dropatom had never been called e getcoord Returns a list x y z of the position of the current atom wrapped in the periodic cell if there is one in the current wrapping mode as specified by wrapmode e getcell Returns a list of 1 4 vectors containing the cell origin center and as many basis vectors as exist i e ox oy oz ax ay az bx by bz cx cy cz It is more efficient to set the wrapping mode than to do periodic image calculations in Tcl e getmass Returns the mass of the current atom e getcharge Returns the charge of the current atom e getid Returns the 1 based ID of the current atom e addf
88. 1 and cylindricalBCk1 must be defined and cylindricalBCAxis cylindricalBCexpl cylindricalBCr2 cylindricalBC12 cylindricalBCk2 and cylindricalBCexp2 can op tionally be defined e cylindricalBCCenter lt center of cylinder A gt Acceptable Values position Description Location around which cylinder is centered e cylindricalBCAxis lt axis of cylinder A gt Acceptable Values x y or z Description Axis along which cylinder is aligned 74 cylindricalBCr1 lt radius for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect along the non axis plane of the cylinder cylindricalBC11 lt distance along cylinder axis for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect along the cylinder axis cylindricalBCk1 lt force constant for first potential gt Acceptable Values non zero decimal Description Force constant for the first harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center cylindricalBCexp1 lt exponent for first potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for first boundary potential The only likely values to use are 2 and 4 cylindricalBCr2 lt radius for se
89. 1 4 DCD trajectory files NAMD produces DCD trajectory files in the same format as X PLOR and CHARMM The DCD files are single precision binary FORTRAN files so are transportable between computer architec tures The file readers in NAMD and VMD can detect and adapt to the endianness of the machine on which the DCD file was written and the utility program flipdcd is also provided to reformat these files if needed The exact format of these files is very ugly but supported by a wide range of analysis and display programs The timestep is stored in the DCD file in NAMD internal units and must be multiplied by TIMEFACTOR 48 88821 to convert to fs Positions in DCD files are stored in A Velocities in DCD files are stored in NAMD internal units and must be multiplied by PDBVELFACTOR 20 45482706 to convert to A ps Forces in DCD files are stored in kcal mol A 22 3 1 5 NAMD binary files NAMD uses a trivial double precision binary file format for coordinates velocities and forces Due to its high precision this is the default output and restart format VMD refers to these files as the namdbin format The file consists of the atom count as a 32 bit integer followed by all three position or velocity components for each atom as 64 bit double precision floating point i e NXYZXYZXYZXYZ where N is a 4 byte int and X Y and Z are 8 byte doubles If the number of atoms the file contains is known then the atom count can be used to determine endiannes
90. 178 180 180 180 181 183 187 187 187 187 187 188 189 189 189 191 191 192 196 198 17 4 Linux or Other Unix Workstation Networks o 17 5 Shared Memory and Network Based Parallelism SMP Builds 10 Cray ALAMOS ica a AA ong ah ot BO Ee A Hd Te S GELATIN eile Ses eos A Ae Shae pt Bote 17 8 IBM POWER Clusters 1729 CRU ALAN 0 koe a8 ae Soe ele TR Ae ae ee wee ba ee A 17 10CUDA GPU Acceleration 17 11Xeon Phi Acceleration I ADMemory Usager dolia o A A o e ah ee 17 13Improving Parallel Scaling e 18 NAMD Availability and Installation 18 1 How to obtain NAMD 2 ee 18 2 Platforms on which NAMD will currently run o 18 3 Installing NAM Disa a png ke til ee A A ne PO eS 18 4 Compiline NA MID ooo Ponds BAL eee ae a Be oe eS eg 1825 Documentations o os 4 202 sees os dee OR Pasa SON Pn RSE en Pat eae Bo pes References Index 10 211 211 211 211 212 212 213 219 List of Figures NOT BR WN FR 10 11 Graph of van der Waals potential with and without switching Graph of electrostatic potential with and without shifting function Graph of electrostatic split between short and long range forces Example of cutoff and pairlist distance uses 2 2 Graph showing a slice of a ramp potential showing the effect of mgridforcevoff Graphical representation of
91. 2 2005 Electronic documents will include a direct link to the official NAMD page http www ks uiuc edu Research namd One copy of each publication or report will be supplied to Illinois at the addresses listed below in Contact Information 7 Should Licensee wish to make commercial use of the Software Licensee will contact Illinois namd ks uiuc edu to negotiate an appropriate license for such use Commercial use includes 1 integration of all or part of the Software into a product for sale lease or license by or on behalf of Licensee to third parties or 2 distribution of the Software to third parties that need it to commercialize product sold or licensed by or on behalf of Licensee 8 Government Rights Because substantial governmental funds have been used in the devel opment of NAMD any possession use or sublicense of the Software by or to the United States government shall be subject to such required restrictions 9 NAMD is being distributed as a research and teaching tool and as such TCBG encourages contributions from users of the code that might at Illinois sole discretion be used or incorporated to make the basic operating framework of the Software a more stable flexible and or useful product Licensees that wish to contribute their code to become an internal portion of the Software may be required to sign an Agreement Regarding Contributory Code for NAMD Software before Illinois can accept it contact namd ks uiu
92. 2 and 3 are idle but if either of threads 2 or 3 are active the core is split four ways The fastest configuration of 32 threads or processes on a 128 thread 32 core is therefore setcpuaffinity pemap 0 127 4 For 64 threads we need cores 0 1 4 5 8 9 or 0 127 4 2 Running 4 processes with ppn 31 would be setcpuaffinity pemap 0 127 32 31 commap 31 127 32 207 For an Altix UV or other machines where the queueing system assigns cores to jobs this infor mation must be obtained with numactl show and passed to NAMD in order to set thread affinity which will improve performance namd2 setcpuaffinity numactl show awk physcpubind printf p d pemap d NF 1 2 for i 3 i lt NF i printf 7 d i 17 10 CUDA GPU Acceleration Energy evaluation is slower than calculating forces alone and the loss is much greater in CUDA accelerated builds Therefore you should set output Energies to 100 or higher in the simulation config file Some features are unavailable in CUDA builds including alchemical free energy perturbation and the Lowe Andersen thermostat As this is a new feature you are encouraged to test all simulations before beginning production runs Forces evaluated on the GPU differ slightly from a CPU only calculation an effect more visible in reported scalar pressure values than in energies To benefit from GPU acceleration you will need a CUDA build of NAMD and a recent high end NVIDIA video
93. 35 542 1977 T C Beutler A E Mark R C van Schaik P R Gerber and W F van Gunsteren Avoid ing singularities and numerical instabilities in free energy calculations based on molecular simulations Chem Phys Lett 222 529 539 1994 D L Beveridge and F M DiCapua Free energy via molecular simulation Applications to chemical and biomolecular systems Annu Rev Biophys Biophys 18 431 492 1989 A Bondi van der Waals volumes and radii J Phys Chem 68 441 451 1964 S Boresch and M Karplus The role of bonded terms in free energy simulations I theoretical analysis J Phys Chem A 103 103 118 1999 D Branduardi F L Gervasio and M Parrinello From a to b in free energy space J Chem Phys 126 5 054103 2007 B R Brooks R E Bruccoleri B D Olafson D J States S Swaminathan and M Karplus CHARMM a program for macromolecular energy minimization and dynamics calculations J Comp Chem 4 2 187 217 1983 A T Br nger X PLOR Version 3 1 A System for X ray Crystallography and NMR The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry Yale University 1992 G Bussi A Laio and M Parrinello Equilibrium free energies from nonequilibrium metady namics Phys Rev Lett 96 9 090601 2006 A Carter E G Ciccotti J T Hynes and R Kapral Constrained reaction coordinate dynamics for the simulation of rare events Chem Phys Lett 156
94. 472 477 1989 C Chipot and D A Pearlman Free energy calculations the long and winding gilded road Mol Sim 28 1 12 2002 213 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 C Chipot and A Pohorille editors Free energy calculations Theory and applications in chemistry and biology Springer Verlag 2007 G Ciccotti R Kapral and E Vanden Eijnden Blue moon sampling vectorial reaction coor dinates and unbiased constrained dynamics ChemPhysChem 6 9 1809 1814 2005 E A Coutsias C Seok and K A Dill Using quaternions to calculate RMSD J Comput Chem 25 15 1849 1857 2004 E Darve D Rodr guez G mez and A Pohorille Adaptive biasing force method for scalar and vector free energy calculations J Chem Phys 128 14 144120 2008 W K den Otter Thermodynamic integration of the free energy along a reaction coordinate in cartesian coordinates J Chem Phys 112 7283 7292 2000 Y Deng and B Roux Computations of standard binding free energies with molecular dynamics simulations J Phys Chem B 113 8 2234 2246 2009 G Fiorin M L Klein and J H nin Using collective variables to drive molecular dynamics simulations Mol Phys 111 22 23 3345 3362 2013 D Frenkel and B Smit Understanding Molecular Simulation From Algorithms to Applications Academic Press California 2002 J Gao K Kuczera B Tidor and M Karplus Hidden
95. AMBER force field parameters 2 2 0 ee ee 3 4 GROMACS force field parameters 0002 eee ee ee eee Creating PSF Structure Files AN Ordinary Usage a oe Rela a Pa ee lg tee oe Sec O 4 1 1 Preparing separate PDB files o 2002000 4 1 2 Deleting unwanted atoms 0000 eee ee 4 9 BPT Example 04 28 Solty Geb iced ot ates eS a att i 4 3 Building solvent around a protein osaa aa ee AA Listrof Commands seos i s a bad a A Oe Bas 4 5 Example of a Session Log np acson eu m o y a a E ee Force Field Parameters 5 1 Potential energy functions oaoa 5 1 1 Bonded potential energy terms e 5 1 2 Nonbonded potential energy terms oaoa ooa a a 5 2 Non bonded interactions 5 2 1 Van der Waals interactions e 5 2 2 Electrostatic interactions ee 5 2 3 Non bonded force field parameters 0 0 2 00200004 5 2 4 PME parameters EL y a a DAE a a E a a EA 5 2 5 MSM parameters e 12 12 14 15 15 15 15 16 19 20 22 22 22 22 22 22 23 23 23 24 26 28 30 32 32 33 33 34 38 39 45 5 3 5 4 5 9 5 6 6 1 6 2 6 3 7 1 7 2 7 3 7 4 7 5 5 2 6 Full direct parameters a 5 2 7 Tabulated nonbonded interaction parameters Water Models oxida ad Drude polarizable force field 2 2 o o e 5 4 1 Required input filles e 5 42 Standard
96. Am Chem Soc 120 23 5771 5782 1998 C Simmerling M R Lee A R Ortiz A Kolinski J Skolnick and P A Kollman Com bining MONSSTER and LES PME to predict protein structure from amino acid sequence Application to the small protein CMTI 1 J Am Chem Soc 122 35 8392 8402 2000 R D Skeel and J J Biesiadecki Symplectic integration with variable stepsize Ann Numer Math 1 191 198 1994 J Srinivasan M W Trevathan P Beroza and D A Case Application of a pairwise gen eralized born model to proteins and nucleic acids inclusion of salt effects Theor Chem Acc 101 426 434 1999 W C Still A Tempczyk R C Hawley and T Hendrickson Semianalytical treatment of solvation for molecular mechanics and dynamics J Am Chem Soc 112 6127 6129 1990 T P Straatsma and J A McCammon Multiconfiguration thermodynamic integration J Chem Phys 95 1175 1118 1991 T P Straatsma and J A McCammon Computational alchemy Annu Rev Phys Chem 43 407 435 1992 B T Thole Molecular polarizabilities calculated with a modified dipole interaction Chem Phys 59 341 350 1981 P Van Duijnen and M Swart Molecular and atomic polarizabilities Thole s model revisited J Phys Chem A 102 14 2399 2407 1998 W F van Gunsteren Methods for calculation of free energies and binding constants Successes and problems In W F Van Gunsteren and P K Weiner editors Computer simulation of biomol
97. D s atom coordinates with the coordinates in the frame and returns O if successful or 1 if end of file was reached coorfile skip skips past one frame in the DCD file this is significantly faster than reading coordinates and throwing them away coorfile close closes the file The coorfile command is not available on the Cray T3E Force and energy analysis are especially useful in the context of pair interaction calculations see Sec 14 1 for details as well as the example scripts in Sec 16 Please note that while NAMD has traditionally allowed comments to be started by a appear ing anywhere on a line Tcl only allows comments to appear where a new statement could begin With Tcl config file parsing enabled all shipped binaries both NAMD and Tcl comments are allowed before the first run command At this point only pure Tcl syntax is allowed In addition the idiom for Tcl comments will only work with Tcl enabled NAMD has also traditionally allowed parameters to be specified as param value This is supported but only before the first run command Some examples this is my config file lt OK reassignFreq 100 how often to reset velocities lt only w Tcl reassignTemp 20 temp to reset velocities to lt OK before run run 1000 lt now Tcl only reassignTemp 40 temp to reset velocities to lt is required NAMD has also traditionally allowed parameters to be specified as
98. DRCOMAVG gives the average temperature averaged since the previously reported temperature for the warm center of mass degrees of freedom DRBONDAVG gives the average temperature averaged since the previously reported temperature for the cold Drude oscillator degrees of freedom The energies resulting from the Drude oscillators and the anisotropic interactions are summed into the BOND energy The energies resulting from the LPs and the screened Coulomb interactions of Thole are summed into the ELECT energy 5 4 3 Drude force field parameters The Drude model should be used with the Langevin thermostat enabled Langevin on Doing so permits the use of normal sized time steps e g 1 fs The Drude model is also compatible with constant pressure simulation using the Langevin piston Long range electrostatics may be calculated using PME The nonbonded exclusions should generally be set to use either the 1 3 exclusion policy exclude 1 3 or the scaled 1 4 exclusion policy exclude scaled1 4 The Drude water model SWM4 NDP is a 5 site model with four charge sites and a nega tively charged Drude particle 44 with the particles ordered in the input files as oxygen Drude particle LP hydrogen hydrogen The atoms in the water molecules should be constrained 59 rigidBonds water with use of the SETTLE algorithm recommended useSettle on Ex plicitly setting the water model waterModel swm4 is optional e drude lt Perform integratio
99. Ewald coefficient and the overall accuracy of the results e PMEInterpOrder lt PME interpolation order gt Acceptable Values positive integer 51 Default Value 4 cubic Description Charges are interpolated onto the grid and forces are interpolated off using this many points equal to the order of the interpolation function plus one PMEGridSpacing lt maximum space between grid points gt Acceptable Values positive real Description The grid spacing partially determines the accuracy and efficiency of PME If any of the grid sizes below are not set then PMEGridSpacing must be set recommended value is 1 0 A and will be used to calculate them If a grid size is set then the grid spacing must be at least PMEGridSpacing if set or a very large default of 1 5 PMEGridSizeX lt number of grid points in x dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeX should have only small integer factors 2 3 and 5 PMEGridSizeY lt number of grid points in y dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeY should have only small integer factors 2 3 and 5 PMEGridSizeZ lt number of grid points in z dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and
100. If such configurations are expected consider defining a tilt colvar using the same axis e and restraining it with a lower wall away from 1 tilt cosine of the rotation orthogonal to a given axis The component tilt measures the cosine of the angle of the tilt sub rotation which combined with the spin sub rotation provides the complete rotation of a group of atoms The cosine of the tilt angle rather than the tilt angle itself is implemented because the latter is unevenly distributed even for an isotropic system consider as an analogy the angle 9 in the spherical coordinate system The component tilt relies on the same options as spinAngle including the definition of the axis e The values of tilt are real numbers in the interval 1 1 the value 1 represents an orientation fully parallel to e tilt angle 0 and the value 1 represents an anti parallel orientation alpha a helix content of a protein segment The block alpha defines the parameters to calculate the helical content of a segment of protein residues The a helical content across the N 1 residues No to No N is calculated by the formula oy cH O No NotI O No 1 N No 5 OF Q No 5 NO EN Eu 44 1 No N 2 1 No N 4 ae ee A n C n 1 A n 2 ee hbf n y n 4 2 N 2 x anpi cs a ae N A 2 i o 45 where the score function for the Ca Ca Ca angle is defined as 2 ia a O Ed alta 00 Abro angf
101. InterpType parameter 58 tabulatedEnergies parameter 57 tabulatedEnergiesFile parameter 57 targetCenters colvars harmonic keyword 158 targetEquilSteps colvars harmonic keyword 160 targetForceConstant colvars harmonic key word 160 targetForceExponent colvars harmonic key word 160 targetNumStages colvars harmonic keyword 159 targetNumSteps colvars harmonic keyword 158 tclBC parameter 109 tclBCArgs parameter 109 tclBCScript parameter 109 tclForces parameter 105 tclForcesScript parameter 105 tCouple parameter 81 tCoupleCol parameter 81 tCoupleFile parameter 81 tCoupleTemp parameter 81 TEMPAVG 27 temperature parameter 77 timestep parameter 77 TMD parameter 101 TMDDiffRMSD parameter 102 TMDFile parameter 102 TMDFile2 parameter 103 TMDFinalRMSD parameter 102 TMDFirstStep parameter 102 TMDInitialRMSD parameter 102 TMDk parameter 101 TMDLastStep parameter 102 TMDOutputFreq parameter 101 topology alias psfgen command 39 topology psfgen command 39 TOTAL2 energy 27 TOTALS energy 27 twoAwayX 210 twoAwayY 210 twoAwayZ 210 units used for output 22 23 26 updateBias colvars abf keyword 150 updateFrequency colvars alb keyword 162 upperBoundary colvars colvar keyword 119 upper Wall colvars colvar keyword 121 upper WallConstant colvars colvar keyword 120 useConstantArea parameter 17 84 useConstantRatio parameter 17 84 useF lexibleCell parameter 17 84
102. LowerBoundary e expandBoundaries lt Allow to expand the two boundaries if needed gt Context colvar Acceptable Values boolean Default Value off Description If defined biasing and analysis methods may keep their own copies of lowerBoundary and upperBoundary and expand them to accommodate values that do not fit in the initial range Currently this option is used by the metadynamics bias 10 5 2 to keep all of its hills fully within the grid This option cannot be used when the initial boundaries already span the full period of a periodic colvar 10 2 2 Artificial boundary potentials walls The following options are useful to define restraints confining potentials for this colvar To apply moving restraints or restraints to more than one colvar simultaneously a more convenient option is to use the harmonic bias 10 5 3 When using an extended Lagrangian the boundary potential is applied to the actual colvar in contrast with forces for all types of biases which are applied to the extended coordinate e lowerWallConstant lt Lower wall force constant kcal mol U gt Context colvar Acceptable Values positive decimal Description Defines the force constant for a confining restraint on the colvar in the form of a half harmonic potential The potential starts at lowerWal11 if it is defined or lowerBoundary otherwise The energy unit of the constant is kcal mol while the spatial unit U is that of the colvar e l
103. Note The PDB file has limited precision and fixed point numbers in some cases the vector may not be accurately represented and vector should be used instead e vectorCol lt PDB column used to flag participating atoms gt Context eigenvector Acceptable Values 0 or B Description Analogous to atomsCol e vectorColValue lt Value used to flag participating atoms in the PDB file gt Context eigenvector Acceptable Values positive decimal Description Analogous to atomsColValue e differenceVector lt The 3n dimensional vector is the difference between vector and refPositions gt Context eigenvector Acceptable Values boolean Default Value off Description If this option is on the numbers provided by vector or vectorFile are interpreted as another set of positions x the vector v is then defined as v x a 138 This allows to conveniently define a colvar as a projection on the linear transformation between two sets of positions A and B For convenience the vector is also normalized so that 0 when the atoms are at the set of positions A and 1 at the set of positions B This component returns a number in A whose value ranges between the smallest and largest abso lute positions in the unit cell during the simulations see also distanceZ Due to the normalization in eq 40 this range does not depend on the number of atoms involved gyration radius of gyration of a group
104. S RB dihedrals are supposed to imply exclusions but NAMD does not support this e Constraints restraints and settles are not implemented in NAMD e In some cases it may not work to override some but not all of the parameters for a bond atom etc In this case NAMD will generate an error and stop The parser will sometimes not tolerate correct GROMACS files or fail to detect errors in badly formatted files e NAMD does not support all the types of bond potentials that exist in GROMACS but approximates them with harmonic or sinusoidal potentials e NAMD does not read periodic box lengths in the coordinate file They must be explicitly specified in the NAMD configuration file 31 4 Creating PSF Structure Files The psfgen structure building tool consists of a portable library of structure and file manipulation routines with a Tcl interface Current capabilities include e reading CHARMM topology files e reading psf files in X PLOR NAMD format e extracting sequence data from single segment PDB files e generating a full molecular structure from sequence data e applying patches to modify or link different segments e writing NAMD and VMD compatible PSF structure files e extracting coordinate data from PDB files e constructing guessing missing atomic coordinates e deleting selected atoms from the structure e writing NAMD and VMD compatible PDB coordinate files We are currently refining the interface of psfgen and adding feature
105. The grid padding applies only to non periodic dimensions for which the extent of the grid is automatically determined by the maximum and minimum of the initial coordinates plus the padding value MSMxmin MSMymin MSMzmin lt minimum x y z coordinate A gt Acceptable Values real Description Set independently the minimum x y or z coordinates of the simulation This parameter is applicable only to non periodic dimensions It is useful in conjunction with setting a boundary restraining force with Tcl boundary forces in Sec 9 11 MSMxmax MSMymax MSMzmax lt maximum x y z coordinate A gt Acceptable Values real Description Set independently the maximum x y or z coordinates of the simulation This parameter is applicable only to non periodic dimensions It is useful in conjunction with setting a boundary restraining force with Tcl boundary forces in Sec 9 11 MSMBlockSizeX MSMBlockSizeY MSMBlockSizeZ lt block size for grid decomposition gt Acceptable Values positive integer Default Value 8 55 Description Tune parallel performance by adjusting the block size used for parallel domain decomposition of the grid Recommended to keep the default e MSMSerial lt Use serial long range solver gt Acceptable Values yes or no Default Value no Description Enable instead the slow serial long range solver Intended to be used only for testing and diagnostic purposes 5 2 6 Full direct parameters The dir
106. The recommended value is 40000 fitted from QM calculations e drudeNbTholeCut lt nonbonded Thole interaction radius A gt Acceptable Values positive decimal Description If drudeNbTholeCut is defined the screened Coulomb correction of Thole is also calculated for non excluded nonbonded pairs of Drude oscillators that are within this radius of interaction The recommended value is 5 0 A 5 5 MARTINI Residue Based Coarse Grain Forcefield The MARTINI forcefield for residue based coarse grain models allows simulation of several tens of atoms as only several large coarse grained particles 49 50 52 In the MARTINI model each protein residue is represented by a backbone bead and usually one or more sidechain beads When preparing MARTINI simulations it is important to include only those dihedrals specified by the forcefield Using the auto dihedrals or regenerate dihedrals feature of psfgen will create dihedrals for all possible sets of four bonded atoms This is incorrect for MARTINI and will result in energy jumps because the dihedral potential function is degenerate for the angles of 180 degrees allowed by cosine based angles When using MARTINI the following configuration parameters should be set as indicated 60 cosAngles on martiniSwitching on dielectric 15 0 PME off e cosAngles lt enable the MARTINI cosine based angle potential function gt Acceptable Values on or off Default Value off Description Specifi
107. UNIX filename Description This file contains the coordinates of all the atoms Note that coordinates can also be used for PDB format coordinate file When gromacs is set to on either grocoorfile or coordinates must be defined but not both To run a SMOG simulation the following extra parameters must be defined e GromacsPair lt Are GROMACS pair forces turned on gt Acceptable Values on or off Default Value off Description This variable determines if the pair section of the GROMACS topology file grotopfile is evaluated Currently only Lennard Jones type pairs are supported Variable is only used if gromacs variable is on e staticAtomAssignment lt Optimization to fix atoms onto a specific node gt Acceptable Values on or off Default Value off Description Specifies if atoms should be statically fixed to a node This will change the internode communication and will give a significant speed up to MD simulations if the atoms are moving rapidly It is suggested that SMOG simulations use the staticAtomAssignment flag 190 14 Runtime Analysis 14 1 Pair interaction calculations NAMD supportes the calculation of interaction energy calculations between two groups of atoms When enabled pair interaction information will be calculated and printed in the standard output file on its own line at the same frequency as energy output The format of the line is PAIR INTERACTION STEP step VDW_FORCE fx fy fz ELECT_FORCE fx fy fz T
108. a of computational chemistry volume 2 pages 1070 1083 Wiley and Sons Chichester 1998 S J Marrink A H de Vries and A E Mark Coarse grained model for semiquantitative lipid simulations J Phys Chem B 108 750 760 2004 S J Marrink H J Risselada S Yefimov D P Tieleman and A H de Vries The martini forcefield coarse grained model for biomolecular simulations J Phys Chem B 111 7812 7824 2007 J A McCammon and S C Harvey Dynamics of Proteins and Nucleic Acids Cambridge University Press Cambridge 1987 L Monticelli S Kandasamy X Periole and R L D T S Marrink The martini coarse grained forcefield extension to proteins J Chem Theor Comp 4 819 834 2008 Y Mu P H Nguyen and G Stock Energy landscape of a small peptide revealed by dihedral angle principal component analysis Proteins 58 1 45 52 2005 J K Noel P C Whitford K Y Sanbonmatsu and J N Onuchic SMOG ctbp simplified deployment of structure based models in GROMACS Nucleic Acids Research 38 W657 61 2010 A Onufriev D Bashford and D A Case Modification of the generalised born model suitable for macromolecules J Phys Chem 104 3712 3720 2000 A Onufriev D Bashford and D A Case Exploring protein native states and large scale conformational changes with a modified generalized born model Proteins Struct Func Gen 55 383 394 2004 D A Pearlman A comparison of alternative appro
109. ach colvar is defined by one or more components typically only one Each component consists of a keyword identifying a functional form and a definition block following that keyword specifying the atoms involved and any additional parameters cutoffs reference values The types of the components used in a colvar determine the properties of that colvar and which biasing or analysis methods can be applied In most cases the colvar returns a real number which is computed by one or more instances of the following components e distance distance between two groups e distanceZ projection of a distance vector on an axis e distanceXY projection of a distance vector on a plane e distanceInv mean distance between two groups of atoms e g NOE based distance e angle angle between three groups e coordNum coordination number between two groups e selfCoordNum coordination number of atoms within a group e hBond hydrogen bond between two atoms e rmsd root mean square deviation RMSD from a set of reference coordinates e eigenvector projection of the atomic coordinates on a vector e orientationAngle angle of the best fit rotation from a set of reference coordinates e orientationProj cosine of orientationProj e spinAngle projection orthogonal to an axis of the best fit rotation from a set of reference coordinates 130 tilt projection on an axis of the best fit rotation from a set of reference coordinates gy
110. aches to free energy calculations J Phys Chem 98 1487 1493 1994 J W Pitera and J D Chodera On the use of experimental observations to bias simulated ensembles J Chem Theory Comput 8 3445 3451 2012 P Raiteri A Laio F L Gervasio C Micheletti and M Parrinello Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics J Phys Chem B 110 8 3533 9 2005 A Roitberg and R Elber Modeling side chains in peptides and proteins Application of the locally enhanced sampling technique and the simulated annealing methods to find minimum energy conformations J Chem Phys 95 9277 9287 1991 M J Ruiz Montero D Frenkel and J J Brey Efficient schemes to compute diffusive barrier crossing rates Mol Phys 90 925 941 1997 M Schaefer and C Froemmel A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution J Mol Biol 216 1045 1066 1990 216 63 64 65 66 67 68 69 70 71 72 73 74 75 76 TT M R Shirts D L Mobley J D Chodera and V S Pande Accurate and efficient corrections for missing dispersion interactions in molecular simulations J Phys Chem B 111 45 13052 13063 2007 C Simmerling T Fox and P A Kollman Use of locally enhanced sampling in free energy calculations Testing and application to the a 8 anomerization of glucose J
111. airInteractionGroupi lt Flag to indicate atoms in group 1 gt Acceptable Values integer Description e pairInteractionGroup2 lt Flag to indicate atoms in group 2 gt Acceptable Values integer Description These options are used to indicate which atoms belong to each interac tion group Atoms with a value in the column specified by pairInteractionCol equal to pairInteractionGroup1 will be assigned to group 1 likewise for group 2 191 14 2 Pressure profile calculations NAMD supports the calculation of lateral pressure profiles as a function of the z coordinate in the system The algorithm is based on that of Lindahl and Edholm JCP 2000 with modifications to enable Ewald sums based on Sonne et al JCP 122 2005 The simulation space is partitioned into slabs and half the virial due to the interaction between two particles is assigned to each of the slabs containing the particles This amounts to employing the Harasima contour rather than the Irving Kirkwood contour as was done in NAMD 2 5 The diagonal components of the pressure tensor for each slab averaged over all timesteps since the previous output are recorded in the NAMD output file The units of pressure are the same as in the regular NAMD pressure output i e bar The total virial contains contributions from up to four components kinetic energy bonded interactions nonbonded interactions and an Ewald sum All but the Ewald sums are computed online during a normal s
112. al angle potential describes the angular spring between the planes formed by the first three and last three atoms of a consecutively bonded i j k l quadruple of atoms DE t cos ny ifn gt 0 5 k py ifn 0 where 4 is the angle in radians between the 7 7 k plane and the j k l plane The integer constant n is nonnegative and indicates the periodicity For n gt 0 is the phase shift angle and k is the multiplicative constant For n 0 acts as an equilibrium angle and the units of k change to potential rad A given i j k quadruple of atoms might contribute multiple terms to the potential each with its own parameterization The use of multiple terms for a torsion angle allows for complex angular variation of the potential effectively a truncated Fourier series 46 5 1 2 Nonbonded potential energy terms The nonbonded potential terms involve interactions between all i j pairs of atoms usually ex cluding pairs of atoms already involved in a bonded term Even using a fast evaluation methods the cost of computing the nonbonded potentials dominates the work required for each time step of an MD simulation The Lennard Jones potential accounts for the weak dipole attraction between distant atoms and the hard core repulsion as atoms become close 12 6 2 6 Tij Tij where rj 7 7 gives the distance between the pair of atoms The parameter Emin Urs Rmin is the minimum of the
113. ame changes to outputName colvars lt name gt lt replicaID gt hills traj This file can be used to quickly visualize the positions of all added hills in case newHillFrequency does not coincide with colvarsRestartFrequency 10 5 3 Harmonic restraints The harmonic biasing method may be used to enforce fixed or moving restraints including variants of Steered and Targeted MD Within energy minimization runs it allows for restrained minimiza tion e g to calculate relaxed potential energy surfaces In the context of the colvars module harmonic potentials are meant according to their textbook definition V a k a ag Note that this differs from harmonic bond and angle potentials in common force fields where the factor of one half is typically omitted resulting in a non standard definition of the force constant The restraint energy is reported by NAMD under the MISC title A harmonic restraint is set up by a harmonic block which may contain in addition to the standard option colvars the following keywords e forceConstant lt Scaled force constant kcal mol gt Context harmonic Acceptable Values positive decimal Default Value 1 0 Description This defines a scaled force constant for the harmonic potential To ensure consistency for multidimensional restraints it is divided internally by the square of the specific width for each colvar involved which is 1 by default so that all colvars are effectively
114. and the functionality of the Tcl language one should be able to perform any on the fly analysis and manipulation To make it easier to perform certain tasks some Tcl routines are provided below Several vector routines vecadd vecsub vecscale from the VMD Tcl interface are defined Please refer to VMD manual for their usage The following routines take atom coordinates as input and return some geometry parameters bond angle dihedral e getbond lt coor1 gt lt coor2 gt Returns the length of the bond between the two atoms Actually the return value is simply the distance between the two coordinates coorl and coor2 are coordinates of the atoms e getangle lt coor1 gt lt coor2 gt lt coor3 gt Returns the angle from 0 to 180 defined by the three atoms coor1 coor2 and coor3 are coordinates of the atoms e getdihedral lt coori gt lt coor2 gt lt coor3 gt lt coor4 gt Returns the dihedral from 180 to 180 defined by the four atoms coor1 coor2 coor3 and coor4 are coordinates of the atoms The following routines calculate the derivatives gradients of some geometry parameters angle dihedral e anglegrad lt coor1 gt lt coor2 gt lt coor3 gt An angle defined by three atoms is a function of their coordinates 0 71 73 73 in radian This command takes the coordinates of the three atoms as input and returns a list of 1 ee oe Each element of the list i
115. ar dynamics MD simulations compute atomic trajectories by solving equations of motion numerically using empirical force fields such as the CHARMM force field that approximate the actual atomic force in biopolymer systems Detailed information about MD simulations can be found in several books such as 1 51 In order to conduct MD simulations various computer programs have been developed including X PLOR 13 and CHARMM 12 These programs were originally developed for serial machines Simulation of large molecules however require enormous computing power One way to achieve such simulations is to utilize parallel computers In recent years distributed memory parallel computers have been offering cost effective computational power NAMD was designed to run efficiently on such parallel machines for simulating large molecules NAMD is particularly well suited to the increasingly popular Beowulf class PC clusters which are quite similar to the workstation clusters for which is was originally designed Future versions of NAMD will also make efficient use of clusters of multi processor workstations or PCs NAMD has several important features 12 e Force Field Compatibility The force field used by NAMD is the same as that used by the programs CHARMM 12 and X PLOR 13 This force field includes local interaction terms consisting of bonded interactions between 2 3 and 4 atoms and pairwise interactions including electrostatic and van der Waals f
116. arning message is printed and the last parameter value read is used Thus the order that files are read can be important in cases where duplicate values appear in separate files e paraTypeXplor lt Is the parameter file in X PLOR format gt Acceptable Values on or off Default Value on Description Specifies whether or not the parameter file s are in X PLOR format X PLOR format is the default for parameter files Caveat The PSF file should be also con structed with X PLOR in case of an X PLOR parameter file because X PLOR stores in formation about the multiplicity of dihedrals in the PSF file See the X PLOR manual for details e paraTypeCharmm lt Is the parameter file in CHARMM format gt Acceptable Values on or off 23 Default Value off Description Specifies whether or not the parameter file s are in CHARMM format X PLOR format is the default for parameter files Caveat The information about multiplicity of dihedrals will be obtained directly from the parameter file and the full multiplicity will be used same behavior as in CHARMM If the PSF file originates from X PLOR consecutive multiple entries for the same dihedral indicating the dihedral multiplicity for X PLOR will be ignored e velocities lt velocity PDB file gt Acceptable Values UNIX filename Description The PDB file containing the initial velocities for all atoms in the simulation This is typically a restart file or final velocity file written b
117. ars global key word 116 colvarsTrajAppend colvars global keyword 116 colvarsTrajFrequency colvars global keyword 116 COMmotion parameter 77 componentCoeff colvars any component key word 145 componentExp colvars any component key word 145 consexp parameter 62 consForceConfig command 18 92 consForceFile parameter 92 consForceScaling parameter 17 92 conskcol parameter 62 conskfile parameter 62 consref parameter 62 constantForce parameter 18 92 constraints parameter 62 constraintScaling parameter 17 63 coord psfgen command 44 coordinates parameter 23 coordpdb psfgen command 44 coorfile command 18 220 corrFunc colvars colvar keyword 123 corrFuncLength colvars colvar keyword 124 corrFuncNormalize colvars colvar keyword 123 corrFuncOffset colvars colvar keyword 124 corrFuncOutputFile colvars colvar keyword 124 corrFuncStride colvars colvar keyword 124 corrFuncType colvars colvar keyword 123 corrFuncWithColvar colvars colvar keyword 123 cosAngles parameter 61 cutoff colvars coordNum keyword 134 cutoff parameter 48 cutoff3 colvars coordNum keyword 135 cwd parameter 24 cylindricalBC parameter 74 cylindricalBCAxis parameter 74 cylindricalBCCenter parameter 74 cylindricalBCexp1 parameter 75 cylindricalBCexp2 parameter 75 cylindricalBCk1 parameter 75 cylindricalBCk2 parameter 75 cylindricalBCl1 parameter 75 cylindricalBCl2 parameter 75 cylindr
118. atedly e g to check if some value has been set you should call replicaYield seconds in between as this will introduce a delay but still enable processing of asynchronous calls from other replicas Potentially blocking functions such as replicaRecv should not be called from within repli caEval nor should functions such as run checkpointLoad Store and replicaAtomSend Recv that would require the simulation of the remote replica to be halted It is allowed to call replicaSend but not replicaSendrecv from within replicaEval since replicaSend is non blocking and one sided but potentially overtaking in this context Rather than polling a remote replica e g for work via replicaEval it is more efficient to register a request via replicaEval and then call replicaRecv to wait for notification The replicaDcdFile command is similar to the dedFile command in that it changes the trajectory output file but the file is actually opened by a different replica partition and may be written to by any other partition that calls replicaDcdFile with the same index but no filename argument If a filename argument is given any file currently associated with the index is closed and a new file created even if the new and old filenames are the same The new file is created only when the next trajectory frame is written not during the replicaDcdFile command itself The caller must ensure that an index is not used before it is associated with a filename and t
119. bgrid within its supergrid In this example the maingrid has two subgrids subgrid 1 and subgrid 4 labeled generation 1 94 The first of these subgrids has two subgrids of its own generation 2 Notice that subgrids are described immediately after their supergrid The min and max attributes are given in units of grid cells of the supergrid For example a subgrid with min O O O max 1 1 1 would redefine 8 cells of its supergrid the space between gridpoints 0 0 0 and 2 2 2 in grid coordinates Following the comment block the maingrid and subgrids are defined in the format described above in the same order as the comment block The following parameters describe the grid based potentials mgridforce lt apply grid forces gt Acceptable Values yes or no Default Value no Description Specifies whether or not any grid forces are being applied mgridforcefile lt tag gt lt PDB file specifying force multipliers and charges for each atomd gt Acceptable Values UNIX file name Description The force on each atom is scaled by the corresponding value in this PDB file By setting the force multiplier to zero for an atom it will not be affected by the grid force mgridforcecol lt tag gt lt column of PDB from which to read force multipliers gt Acceptable Values X Y Z O or B Default Value B Description Which column in the PDB file specified by mgridforcefile contains the scaling factor mgridforcechargecol lt
120. built If the pair list includes only those atoms within the cutoff distance this pair would not be included in the list Now assume that after five timesteps atoms A and B have moved to only 7 9 apart A and B are now within the cutoff distance of each other and should have their non bonded interactions calculated However because the non bonded interactions are based solely on the pair list and the pair list will not be rebuilt for another five timesteps this pair will be ignored for five timesteps causing energy not to be conserved within the system To avoid this problem the parameter pairlistdist allows the user to specify a distance greater than the cutoff distance for pairs to be included in the pair list as shown in Figure 4 Pairs that are included in the pair list but are outside the cutoff distance are simply ignored So in the above example if the pairlistdist were set to 10 0 then the atom pair A and B would be included in the pair list even though the pair would initially be ignored because they are further apart than the cutoff distance As the pair moved closer and entered the cutoff distance because the pair was already in the pair list the non bonded interactions would immediately be calculated and energy conservation would be preserved The value of pairlistdist should be chosen such that no atom pair moves more than pairlistdist cutoff in one cycle This will insure energy conservation and efficiency The pairlistd
121. c edu for a copy Contact Information The best contact path for licensing issues is by e mail to namd ks uiuc edu or send correspondence to NAMD Team Theoretical and Computational Biophysics Group Beckman Institute University of Illinois 405 North Mathews MC 251 Urbana Illinois 61801 USA Contents 1 Introduction 1 1 NAMD and molecular dynamics simulations e e 12 Acknowledgments 2 2 3 ar e ae ear Pee AE A ee ees Getting Started Za What is needed i 4 0 ao hoe hath bei tk Bop aD Abe A nee Rae 2 2 NAMD configuration file 2 2 0 00 0 000 ee ee ee ee 2 2 1 Configuration parameter syntax sosoo oo a ee ee 2 2 2 Tcl scripting interface and features ooo 002000004 2 2 3 Multiple copy replica exchange scripting interface 2 2 4 Required NAMD configuration parameters 28 4 Input and Output Files 3 1 Elle formats A Boe ee a a a ee A ee 3 14 PDB les Tira 0 a De A ee a anA 3 2 X PLOR format PSF Mesy sos gk hae Phas Hpi ade bee a ae a de BES 3 1 3 CHARMM19 CHARMM22 and CHARMM27 parameter files 3 14 DCD trajectory des Vs oa Ee ew hae ee Ay ok BL ee 3 15 NAMD binary files soc d rara Ae he Gwe a ek eile hake 3 2 NAMD configuration parameters ooo a B22 A gt Input files eck a hte Re nary en ce a ee a ee ne ee ae 3 2 2 Output files mi ee ee ba ee E Ee wea eee ae 3 2 3 Standard output lt 2 posa a egos ge Bee ee ete ee ae es 3 3
122. card CUDA builds will not function without a CUDA capable GPU and a driver that supports CUDA 6 0 If the installed driver is too old NAMD will exit on startup with the error CUDA driver version is insufficient for CUDA runtime version Finally if NAMD was not statically linked against the CUDA runtime then the libcudart so file included with the binary copied from the version of CUDA it was built with must be in a directory in your LD_LIBRARY_PATH before any other libcudart so libraries For example when running a multicore binary recommended for a single machine setenv LD_LIBRARY_PATH LD_LIBRARY_PATH or LD_LIBRARY_PATH LD_LIBRARY_PATH export LD_LIBRARY_PATH namd2 p4 lt configfile gt Each namd2 thread can use only one GPU Therefore you will need to run at least one thread for each GPU you want to use Multiple threads can share a single GPU usually with an increase in performance NAMD will automatically distribute threads equally among the GPUs on a node Specific GPU device IDs can be requested via the devices argument on the namd2 command line for example namd2 p4 devices 0 2 lt configfile gt Devices are shared by consecutive threads in a process so in the above example processes 0 and 1 will share device 0 and processes 2 and 3 will share device 2 Repeating a device will cause it to be assigned to multiple master threads either in the same or different processes which is advised against in general
123. cceptable Values yes or no Default Value no Description Specifies whether or not external program forces are applied e extForcesCommand lt Force calculation command gt Acceptable Values UNIX shell command Description This string is the argument to the system function at every forces evaluation and should read coordinates from the file specified by extCoordFilename and write forces to the file specified by extForceFilename e extCoordFilename lt Temporary coordinate file gt Acceptable Values UNIX filename Description Atom coordinates are written to this file which should be read by the extForcesCommand The format is one line of atomid charge x y z for every atom followed by three lines with the periodic cell basis vectors a x a y a z b x b y b z and c x c y c z The atomid starts at 1 not 0 For best performance the file should be in tmp and not on a network mounted filesystem e extForceFilename lt Temporary force file gt Acceptable Values UNIX filename Description Atom forces are read from this file after extForcesCommand in run The format is one line of atomid replace fx fy fz for every atom followed by the energy on a line by itself and then optionally three lines of the virial v xx v xy v xz v yx v yy v yz v zx v zy v zz where e g v xy fx y for a non periodic force The atomid starts at 1 not 0 and all atoms must be present and in order The energy i
124. ch Drude for additional details and parallel performance re sults 5 4 1 Required input files No additional files are required by NAMD to use the Drude polarizable force field However it is presently beyond the capability of the Psfgen tool to generate the PSF file needed to perform a simulation using the Drude model For now CHARMM is needed to generate correct input files The CHARMM force field parameter files specific to the Drude model are required The PDB file must also include the Drude particles mass between 0 1 and 1 0 and the LPs mass 0 The Drude particles always immediately follow their parent atom The PSF file augments the atom section with additional columns that include the Thole and alpha parameters for the screened Coulomb interactions of Thole The PSF file also requires additional sections that list the LPs including their guide atoms and geometry parameters and list the anisotropic interaction terms including their parameters A Drude compatible PSF file is denoted by the keyword DRUDE given along the top line 5 4 2 Standard output The NAMD logging to standard output is extended to provide additional temperature data on the cold and warm degrees of freedom Four additional quantities are listed on the ETITLE and ENERGY lines DRUDECOM gives the temperature for the warm center of mass degrees of freedom DRUDEBOND gives the temperature for the cold Drude oscillator degrees of freedom
125. ching functions to the non bond interactions within the cut off distance which helps to improve energy conservation while AMBER does not use switching functions so it simply truncates the interactions at cutoff However if authentic AMBER cutoff simulations are desired the switching functions could be turned off by specifying switching off in NAMD configuration file 6 NAMD and AMBER may have different default values for some parameters e g the tolerance of SHAKE One should check other sections of this manual for accurate descriptions of the NAMD options Following are two examples of the NAMD configuration file to read AMBER force field and carry out simulation They may help users to select proper NAMD options for AMBER force field For the convenience of AMBER users the AMBER 6 sander input files are given in the left for comparison which would accomplish similar tasks in AMBER Example 1 Non periodic boundary system cutoff simulation AMBER NAMD TITLE gcntrl ntb 0 igb 2 non periodic use cutoff for non bond nstlim 1000 numsteps 1000 Num of total steps ntpr 50 outputEnergies 50 Energy output frequency ntwr 50 restartfreq 50 Restart file frequency ntwx 100 DCDfreq 100 Trajectory file frequency dt 0 001 timestep 1 in unit of fs This is default tempi 0 temperature O Initial temp for velocity assignment cut 10 cutoff 10 switching off Turn off the switching functions scee 1 2 ex
126. clude scaled1 4 1 4scaling 0 833333 1 1 2 default is 1 0 scnb 2 0 scnb 2 This is default gend amber on Specify this is AMBER force field parmfile prmtop Input PARM file ambercoor inpcrd Input coordinate file outputname md Prefix of output files Example 2 Periodic boundary system PME NVE ensemble using SHAKE algorithm AMBER NAMD TITLE gcntrl ntc 2 nt 2 SHAKE to the bond between each hydrogen and it mother atom 29 rigidBonds all tol 0 0005 rigidTolerance 0 0005 Default is 0 00001 nstlim 500 numsteps 500 Num of total steps ntpr 50 outputEnergies 50 Energy output frequency ntwr 100 restartfreq 100 Restart file frequency ntwx 100 DCDfreq 100 Trajectory file frequency dt 0 001 timestep 1 in unit of fs This is default tempi 300 temperature 300 Initial temp for velocity assignment cut 9 cutoff 9 switching off Turn off the switching functions gend gewald PME on Use PME for electrostatic calculation Orthogonal periodic box size a 62 23 cellBasisVector1i 62 23 0 O b 62 23 cellBasisVector2 O 62 23 0 c 62 23 cellBasisVector3 O O 62 23 nfft1 64 PMEGridSizeX 64 nfft2 64 PMEGridSizeY 64 nfft3 64 PMEGridSizeZ 64 ischrgd 1 NAMD doesn t force neutralization of charge gend amber on Specify this is AMBER force field parmfile FILENAME Input PARM file ambercoor FILENAME Input coordinate file outputname PREFIX Prefix of output files exclude scaled1 4 1 4scaling
127. cm OOH cla E i 46 4 1 02 08 CEH 00 Abro and the score function for the O Y N 4 hydrogen bond is defined through a hBond colvar component on the same atoms The options recognized within the alpha block are e residueRange lt Potential a helical residues gt Context alpha Acceptable Values lt Initial residue number gt lt Final residue number gt Description This option specifies the range of residues on which this component should 141 be defined The colvar module looks for the atoms within these residues named CA N and 0 and raises an error if any of those atoms is not found e psfSegID lt PSF segment identifier gt Context alpha Acceptable Values string max 4 characters Description This option sets the PSF segment identifier for the residues specified in residueRange This option is only required when PSF topologies are used e hBondCoeff lt Coefficient for the hydrogen bond term gt Context alpha Acceptable Values positive between O and 1 Default Value 0 5 Description This number specifies the contribution to the total value from the hydrogen bond terms 0 disables the hydrogen bond terms 1 disables the angle terms e angleRef lt Reference Ca Ca Ca angle gt Context alpha Acceptable Values positive decimal Default Value 88 Description This option sets the reference angle used in the score function 46 e angleTol lt Tolerance
128. computations and iii vectors tcl was borrowed from VMD and defines the vector operations used Two examples for running the scripts are included in the directory lib ramd examples The user is encouraged to read the README examples file provided in the same directory In order to turn RAMD on the line source path to your files ramd 4 0 tc1 should be in cluded in the NAMD configuration file Unless the user decides to store the scripts at a different location the path path to your files should point to the lib ramd scripts directory Other wise the user should make sure that the directory path to your files stores all three scripts described above The specific RAMD simulation parameters to be provided in the NAMD configuration file listed below should be preceded by the keyword ramd The default values for these parameters are only given as guidance They are likely not to be suitable for other systems than those the scripts were tested on e ramd debugLevel lt Set debug level of RAMD gt Acceptable Values integer value Default Value 0 Description Activates verbose output if set to an integer greater than 0 Should be used only for testing purposes because the very dense output is full of information only relevant for debugging ramd mdStart lt Start RAMD MD with MD or RAMD gt Acceptable Values yes or no Default Value no Description Specifies if combined RAMD MD simulatio
129. cond boundary condition A gt Acceptable Values positive decimal Description Distance at which the second potential of the boundary conditions takes effect along the non axis plane of the cylinder If this parameter is defined then cylindricalBC12 and spericalBCk2 must also be defined cylindricalBC12 lt radius for second boundary condition A gt Acceptable Values positive decimal Description Distance at which the second potential of the boundary conditions takes effect along the cylinder axis If this parameter is defined then cylindricalBCr2 and spericalBCk2 must also be defined cylindricalBCk2 lt force constant for second potential gt Acceptable Values non zero decimal Description Force constant for the second harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center cylindricalBCexp2 lt exponent for second potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for second boundary potential The only likely values to use are 2 and 4 7 2 Energy Minimization 7 2 1 Conjugate gradient parameters The default minimizer uses a sophisticated conjugate gradient and line search algorithm with much better performance than the older velocity quenching method The method of conjugate gradients 79 is used to select successive search directions starting with the initial gradient which eliminate repeat
130. cs are likely needed e TMD lt Is TMD active gt Acceptable Values on or off Default Value off Description Should TMD steering forces be applied to the system If TMD is enabled TMDk TMDFile and TMDLastStep must be defined in the input file as well e TMDk lt Elastic constant for TMD forces gt Acceptable Values Positive value in kcal mol A Description The value of k in Eq 31 A value of 200 seems to work well in many cases If this setting is omitted the value in the occupancy column of the pdb file specified by TMDFile will be used as the constant for that atom This allows the user to specify the constant on a per atom basis e TMDOutputFreq lt How often to print TMD output gt Acceptable Values Positive integer Default Value 1 Description TMD output consists of lines of the form TMD ts targetRMS currentRMS 101 where ts is the timestep targetRMS is the target RMSD at that timestep and currentRMS is the actual RMSD TMDFile lt File for TMD information gt Acceptable Values Path to PDB file Description Biased atoms are those whose occupancy O is nonzero in the TMD PDB file Fitted atoms are those whose altloc field is not or 0 if present otherwise all biased atoms are fitted The file must contain no more atoms than the structure file and those atoms present must have the exact same index as the structure file i e the file may contain a truncated atom selection index lt N but
131. ct to each node via rsh ssh without typing your password this can be accomplished via a rhosts files in your home directory by an etc hosts equiv file installed by your sysadmin or by a ssh authorized_keys file in your home directory You should confirm that you can run ssh hostname pwd or rsh hostname pwd without typing a password before running NAMD Contact your local sysadmin if you have difficulty setting this up If you are unable to use rsh or ssh then add setenv CONV DAEMON to your script and run charmd or charmd_faceless which produces a log file on every node You should now be able to try running NAMD as charmrun namd2 p lt procs gt lt configfile gt If this fails or just hangs try adding the verbose option to see more details of the startup process You may need to specify the full path to the namd2 binary Charmrun will start the number of processes specified by the p option cycling through the hosts in the nodelist file as 204 many times as necessary You may list multiprocessor machines multiple times in the nodelist file once for each processor You may specify the nodelist file with the nodelist option and the group which defaults to main with the nodegroup option If you do not use nodelist charmrun will first look for nodelist in your current directory and then nodelist in your home directory Some automounters use a temporary mount directory w
132. cted non exclusive non transferable license to use the Software for academic research and internal busi ness purposes only e g not for commercial use see Paragraph 7 below without a fee Licensee agrees to reproduce the copyright notice and other proprietary markings on all copies of the Soft ware Licensee has no right to transfer or sublicense the Software to any unauthorized person or entity However Licensee does have the right to make complimentary works that interoperate with NAMD to freely distribute such complimentary works and to direct others to the TCBG server to obtain copies of NAMD itself 2 Licensee may at its own expense modify the Software to make derivative works for its own academic research and internal business purposes Licensee s distribution of any derivative work is also subject to the same restrictions on distribution and use limitations that are specified herein for Illinois Software Prior to any such distribution the Licensee shall require the recipient of the Licensee s derivative work to first execute a license for NAMD with Illinois in accordance with the terms and conditions of this Agreement Any derivative work should be clearly marked and renamed to notify users that it is a modified version and not the original NAMD code distributed by Illinois 3 Except as expressly set forth in this Agreement THIS SOFTWARE IS PROVIDED AS IS AND ILLINOIS MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES
133. cted by a set of two bonds i e if atom A is bonded to atom B and atom B is bonded to atom C and atom C is bonded to atom D then the atom pair A D would be excluded With the value of scaled1 4 all 1 3 pairs are excluded and all pairs that match the 1 4 criteria are modified The electrostatic interactions for such pairs are modified by the constant factor defined by 1 4scaling The van der Waals interactions are modified by using the special 1 4 parameters defined in the parameter files The value of scaled1 4 is necessary to enable the modified 1 4 VDW parameters present in the CHARMM parameter files 1 4scaling lt scaling factor for 1 4 electrostatic interactions gt Acceptable Values 0 lt decimal lt 1 Default Value 1 0 Description Scaling factor for 1 4 electrostatic interactions This factor is only used when the exclude parameter is set to scaled1 4 In this case this factor is used to modify the electrostatic interactions between 1 4 atom pairs If the exclude parameter is set to anything but scaled1 4 this parameter has no effect regardless of its value dielectric lt dielectric constant for system gt Acceptable Values decimal gt 1 0 Default Value 1 0 Description Dielectric constant for the system A value of 1 0 implies no modification of the electrostatic interactions Any larger value will lessen the electrostatic forces acting in the system nonbondedScaling lt scaling factor for nonbonded forces gt
134. cture or coordinate file since the atom number field in this PDB file will be ignored SMDk lt force constant to use in SMD simulation gt Acceptable Values positive real Description SMD harmonic constraint force constant Must be specified in kcal mol A The conversion factor is 1 kcal mol 69 479 pN A SMDk2 lt force constant for transverse direction to use in SMD simulation gt Acceptable Values positive real Default Value 0 Description SMD transverse harmonic constraint force constant Must be specified in kcal mol A The conversion factor is 1 kcal mol 69 479 pN A SMDVel lt Velocity of the SMD reference position movement gt Acceptable Values nonzero real A timestep Description The velocity of the SMD center of mass movement Gives the absolute value SMDDir lt Direction of the SMD center of mass movement gt Acceptable Values non zero vector Description The direction of the SMD reference position movement The vector does not have to be normalized it is normalized by NAMD before being used SMDOutputFreg lt frequency of SMD output gt Acceptable Values positive integer Default Value 1 Description The frequency in timesteps with which the current SMD data values are printed out Interactive Molecular Dynamics IMD NAMD now works directly with VMD to allow you to view and interactively steer your simulation With IMD enabled you can connect to NAMD at any time during the simulation to vi
135. cy value of 2 0 One now must define three separate Go potentials for intra protein intra nucleic acid and inter protein nucleic acid interactions In terms of chain types this corresponds to 1 between atom pairs fully in chain 1 2 between atom pairs fully in chain 2 3 between atom pairs where one atom is in chain 1 and the other atom is in chain 2 respectively To run Go a minimum of one chain type must be defined 13 1 3 Configuration file modifications The following configuration parameters are used to setup and run a Go simulation e GoForcesOn lt Are Go forces turned on gt Acceptable Values on or off Default Value off Description Specifies whether or not Go forces should be calculated If turned off Go forces will not be calculated If turned on Go forces will be calculated By default the Go forces will be calculated in addition to the electrostatic and van der Waals forces To simulate a system using only Go forces the partial charges and Lennard Jones parameters can be set to zero in the force field files e GoParameters lt Parameter file defining Go potential gt Acceptable Values file 187 Description File contains parameters to define the Go pairwise forces between different chain types All possible chain type pairing combinations must be enumerated Chain types are defined in the GoCoordinates file The format for the GoParameters file is described in the next section e GoCoordinates l
136. d working backwards in can also sometimes reveal the origin of the instability e pairlistdist lt distance between pairs for inclusion in pair lists A gt Acceptable Values positive decimal gt cutoff Default Value cutoff Description A pair list is generated pairlistsPerCycle times each cycle containing pairs of atoms for which electrostatics and van der Waals interactions will be calculated This parameter is used when switching is set to on to specify the allowable distance between atoms for inclusion in the pair list This parameter is equivalent to the X PLOR parameter 89 CUTNb If no atom moves more than pairlistdist cutoff during one cycle then there will be no jump in electrostatic or van der Waals energies when the next pair list is built Since such a jump is unavoidable when truncation is used this parameter may only be specified when switching is set to on If this parameter is not specified and switching is set to on the value of cutoff is used A value of at least one greater than cutoff is recommended stepspercycle lt timesteps per cycle gt Acceptable Values positive integer Default Value 20 Description Number of timesteps in each cycle Each cycle represents the number of timesteps between atom reassignments For more details on non bonded force evaluation see Section 5 2 splitPatch lt how to assign atoms to patches gt Acceptable Values position or hydrogen Default Value hydrogen Description
137. dNum block defines a coordination number similarly to the component coordNum but the function is summed over atom pairs within groupl i groupl j gt i x x do The keywords accepted by selfCoordNum are a subset of those accepted by coordNum namely group1 here defining all of the atoms to be considered cutoff expNumer and expDenon 135 This component returns a dimensionless number which ranges from approximately 0 all inter atomic distances much larger than the cutoff to Ngroup1 X Vgroup1 1 2 all distances within the cutoff For performance reasons group1 should be of limited size because the cost of the loop over all pairs grows as Ne tact hBond hydrogen bond between two atoms The hBond block defines a hydrogen bond implemented as a coordination number eq 37 between the donor and the acceptor atoms Therefore it accepts the same options cutoff with a different default value of 3 3 A expNumer with a default value of 6 and expDenom with a default value of 8 Unlike coordNum it requires two atom numbers acceptor and donor to be defined It returns an adimensional number with values between 0 acceptor and donor far outside the cutoff distance and 1 acceptor and donor much closer than the cutoff rmsd root mean square displacement RMSD from reference positions The block rmsd defines the root mean square replacement RMSD of a group of atoms with respect to a reference st
138. db 4 1 2 Deleting unwanted atoms The delatom command described below allows you to delete selected atoms from the structure It s fine to remove atoms from your structure before building the PSF and PDB files but you should never edit the PSF and PDB files created by psfgen by hand as it will probably mess up the internal numbering in the PSF file Very often the atoms you want to delete are water molecules that are either too far from the solute or else outside of the periodic box you are trying to prepare In either case VMD atom selections can be used to select the waters you want to delete For example Load a pdb and psf file into both psfgen and VMD resetpsf readpsf myfile psf coordpdb myfile pdb mol load psf myfile psf pdb myfile pdb Select waters that are more than 10 Angstroms from the protein set badwater1 atomselect top name OH2 and not within 10 of protein 33 Alternatively select waters that are outside our periodic cell set badwater2 atomselect top name OH2 and x lt 30 or x gt 30 or y lt 30 or gt 30 or z lt 30 or z gt 30 Delete the residues corresponding to the atoms we selected foreach segid badwater1 get segid resid badwater1 get resid 4 delatom segid resid Have psfgen write out the new psf and pdb file VMD s structure and coordinates are unmodified writepsf myfile_chopwater psf writepdb myfile_chopwater pdb 4 2 BPTI Example To actually run this demo requ
139. de name title and e mail of a person with signature authority to authorize and commit the individuals academic or research institution or corporation as necessary to the terms and conditions of the license agreement All parts of the information must be understood and agreed to as part of completing the form Completion of the form is required before software access is granted Pay particular attention to the authorized requester requirements above and be sure that the form submission is authorized by the duly responsible person UNIVERSITY OF ILLINOIS NAMD MOLECULAR DYNAMICS SOFTWARE LICENSE AGREEMENT Upon execution of this Agreement by the party identified below Licensee The Board of Trustees of the University of Illinois Illinois on behalf of The Theoretical and Computational Biophysics Group TCBG in the Beckman Institute will provide the molecular dynamics software NAMD in Executable Code and or Source Code form Software to Licensee subject to the following terms and conditions For purposes of this Agreement Executable Code is the compiled code which is ready to run on Licensee s computer Source code consists of a set of files which contain the actual program commands that are compiled to form the Executable Code 1 The Software is intellectual property owned by Illinois and all right title and interest in cluding copyright remain with Illinois Illinois grants and Licensee hereby accepts a restri
140. e Langevin coupling coefficients for each atom The coefficients can be read from any floating point column of the PDB file A value of 0 indicates that the atom will remain unaffected 7 4 2 Temperature coupling parameters NAMD is capable of performing temperature coupling in which forces are added or reduced to simulate the coupling of the system to a heat bath of a specified temperature This capability is based on that implemented in X PLOR which is detailed in the X PLOR User s Manual 13 e tCouple lt perform temperature coupling gt Acceptable Values on or off Default Value off Description Specifies whether or not temperature coupling is active If set to on then the parameter tCoupleTemp must be set and the parameters tCoupleFile and tCoupleCol can optionally be set to control the behavior of this feature e tCoupleTemp lt temperature for heat bath K gt Acceptable Values positive decimal Description Temperature to which atoms affected by temperature coupling will be ad justed This temperature will be roughly maintained across the affected atoms through the addition of forces e tCoupleFile lt PDB file with tCouple parameters gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to use for the temperature coupling coefficient for each atom If this parameter is not specified then the PDB file specified by coordinates is used e tCoupleCol lt column of PDB from which to read coe
141. e MPI libraries are very often incompatible between versions you will likely need to recompile NAMD and its underlying Charm libraries to use these machines in parallel the provided non MPI binaries should still work for serial runs The provided charmrun program for these platforms is only a script that attempts to translate charmrun options into mpirun options but due to the diversity of MPI libraries it often fails to work 17 4 Linux or Other Unix Workstation Networks The same binaries used for individual workstations as described above other than pure multicore builds and MPI builds can be used with charmrun to run in parallel on a workstation network The only difference is that you must provide a nodelist file listing the machines where namd2 processes should run for example group main host brutus host romeo The group main line defines the default machine list Hosts brutus and romeo are the two machines on which to run the simulation Note that charmrun may run on one of those machines or charmrun may run on a third machine All machines used for a simulation must be of the same type and have access to the same namd2 binary By default the rsh command is used to start namd2 on each node specified in the nodelist file You can change this via the CONV_RSH environment variable i e to use ssh instead of rsh run setenv CONV_RSH ssh or add it to your login or batch script You must be able to conne
142. e a group s center of geometry with a user defined position 10 3 2 Moving frame of reference The following options define an automatic calculation of an optimal translation centerReference or optimal rotation rotateReference that superimposes the positions of this group to a provided set of reference coordinates This can allow for example to effectively remove from certain colvars the effects of molecular tumbling and of diffusion Given the set of atomic positions x the colvar can be defined on a set of roto translated positions x R x x x x is the geometric center of the x R is the optimal rotation matrix to the reference positions and x is the geometric center of the reference positions Components that are defined based on pairwise distances are naturally invariant under global roto translations Other components are instead affected by global rotations or translations how ever they can be made invariant if they are expressed in the frame of reference of a chosen group of atoms using the centerReference and rotateReference options Finally a few components are defined by convention using a roto translated frame e g the minimal RMSD for these com ponents centerReference and rotateReference are enabled by default In typical applications the default settings result in the expected behavior e centerReference lt Implicitly remove translations for this group gt Context atom group Acceptable Valu
143. e at any position after that many keywords are nested and are only meaningful within a specific context for every keyword documented in the following the parent keyword that defines such context is also indicated in parentheses unlike in the NAMD main configuration file the deprecated sign between a keyword and its value is not allowed unlike in the NAMD main configuration file Tcl commands and variables are not available but it is possible to use Tcl to generate a new configuration file with different parameters see 10 1 1 if a keyword requiring a boolean value yes on true or no off false is provided without an explicit value it defaults to yes on true for example outputAppliedForce may be used as shorthand for outputAppliedForce on the hash character indicates a comment all text in the same line following this character will be ignored 115 The following keywords are available in the global context of the colvars configuration i e they are not nested inside other keywords e colvarsTrajFrequency lt Colvar value trajectory frequency gt Context global Acceptable Values positive integer Default Value 100 Description The values of each colvar and of other related quantities if requested are written to the file outputName colvars traj every these many steps throughout the simulation If the value is 0 such trajectory file is not written For optimization the output is buff
144. e atoms block see 10 3 The latter and related fitting options for the atom group are normally not needed and should be omitted altogether except for advanced usage cases 136 e refPositionsFile lt Reference coordinates file gt Context rmsd Acceptable Values UNIX filename Description This option mutually exclusive with refPositions sets the PDB file name for the reference coordinates to be compared with The format is the same as that provided by refPositionsFile within an atom group definition e refPositionsCol lt PDB column containing atom flags gt Context rmsd Acceptable Values 0 B X Y or Z Description If refPositionsFile is defined and the file contains all the atoms in the topology this option may be povided to set which PDB field is used to flag the reference coordinates for atoms e refPositionsColValue lt Atom selection flag in the PDB column gt Context rmsd Acceptable Values positive decimal Description If defined this value identifies in the PDB column refPositionsCol of the file refPositionsFile which atom positions are to be read Otherwise all positions with a non zero value are read This component returns a positive real number in A Advanced usage of the rmsd component In the standard usage as described above the rmsd component calculates a minimum RMSD that is current coordinates are optimally fitted onto the same reference coordinates that are used to compute the RMSD value
145. e been reached the centers resp force constant are kept fixed In multi stage transformations this sets the number of MD steps per stage e outputCenters lt Write the current centers to the trajectory file gt Context harmonic 158 Acceptable Values boolean Default Value off Description If this option is chosen and colvarsTrajFrequency is not zero the positions of the restraint centers will be written to the trajectory file during the simulation This option allows to conveniently extract the PMF from the colvars trajectory files in a steered MD calculation e outputAccumulatedWork lt Write the accumulated work of the moving restraint to the trajectory file gt Context harmonic Acceptable Values boolean Default Value off Description If this option is chosen targetCenters is defined and colvarsTrajFrequency is not zero the accumulated work from the beginning of the simulation will be written to the trajectory file If the simulation has been continued from a previous state file the previously accumulated work is included in the integral This option allows to conveniently extract the PMF from the colvars trajectory files in a steered MD calculation Note on restarting moving restraint simulations Information about the current step and stage of a simulation with moving restraints is stored in the restart file state file Thus such simulations can be run in several chunks and restarted directly using the same colva
146. e between two groups projected onto an axis or the position of a group along such an axis The axis can be defined using either one reference group and a constant vector or dynamically based on two reference groups main lt Main group of atoms gt Context distanceZ distanceXY Acceptable Values Block main Description Group of atoms whose position r is measured ref lt Reference group of atoms gt Context distanceZ distanceXY Acceptable Values Block ref Description Reference group of atoms The position of its center of mass is noted r below ref2 lt Secondary reference group gt Context distanceZ distanceXY Acceptable Values Block ref2 Default Value none Description Optional group of reference atoms whose position r can be used to define a dynamic projection axis e r2 ril x ra r In this case the origin is rm 1 2 r1 r2 and the value of the component is e r rm axis lt Projection axis A gt Context distanceZ distanceXY Acceptable Values x y z triplet Default Value 0 0 0 0 1 0 Description The three components of this vector define when normalized a projection axis e for the distance vector r r joining the centers of groups ref and main The value of the component is then e r r1 The vector should be written as three components separated by commas and enclosed in parentheses forceNoPBC lt Calculate absolute rathe
147. e containing the free energy alchOutFreq 5 Frequency at which fepOutFreq is updated alchEquilSteps 5000 Number of equilibration steps per A state set Lambda0 0 0 Starting value of A set dLambda 0 1 Increment of A i e dl while LambdaO lt 1 0 4 alchLambda Lambda0 set Lambda0 expr Lambda0 dLambda 2 increment A alchLambda2 Lambda0 3 set lambda2 value pe 10000 4 run 10 000 MD steps The user should be reminded that by setting run 10000 10 000 MD steps will be performed which includes the preliminary fepEquilSteps equilibration steps This means that here the ensemble average of equation 60 will be computed over 5 000 MD steps Alternatively A states may be declared explicitly avoiding the use of TCL scripting TCL script to increment A 1 set lambda value alchLambda 0 0 1 set alchLambda value alchLambda2 0 1 2 set alchLambda2 value run 10000 3 run 10 000 MD steps This option is generally preferred to set up windows of diminishing widths as A gt 0 or 1 a way to circumvent end point singularities caused by appearing atoms that may clash with their 171 surroundings The following second input is proposed for the measuring via TI the free energy of a particle insertion alch On Enable alchemical simulation module alchType ti Set method to thermodynamic integration alchFile ion alch pdb PDB file with perturbation flags alchCol B Perturbation flags in Beta column alchOutfile
148. e reduced to correspond with the reduced potential This option affects velocity initialization reinititialization reassignment and the target temperature for langevin dynamics Langevin dynamics is recommended with 180 this option since in a constant energy simulation energy will flow into the enhanced degrees of freedom until they reach thermal equilibrium with the rest of the system The reduced temperature atoms will have reduced velocities as well unless lesReduceMass is also enabled e lesReduceMass lt reduce enhanced atom mass gt Acceptable Values on or off Default Value off Description Used with lesReduceTemp to restore velocity distribution to enhanced atoms If used alone enhanced atoms would move faster than normal atoms and hence a smaller timestep would be required e lesFile lt PDB file containing LES flags gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to specify the LES image number of each atom If this parameter is not specified then the PDB file containing initial coordinates specified by coordinates is used e lesCol lt column of PDB file containing LES flags gt Acceptable Values X Y Z 0 or B Default Value B Description Column of the PDB file to specify the LES image number of each atom This parameter may specify any of the floating point fields of the PDB file either X Y Z occupancy or beta coupling temperature coupling A value of 0 in this colu
149. e simulation over the A value range of 0 1 0 alchElecLambdaStart At A 0 electrostatic interactions are fully coupled to the simulation and then linearly decreased with increasing A such that at A values greater than or equal to 1 0 alchElecLambdaStart electrostatic interactions are completely decoupled from the simulation Two examples shown in Figure 9 describe the relationship between the user defined value of A and the coupling of electrostatic or vdW interactions to the simulation e alchVdwLambdaEnd lt Value of A to cancel van der Waals interactions gt Acceptable Values positive decimal Default Value 1 0 Description If the alchElecLambdaStart option is used it may also be desirable to separate the scaling of van der Waals and electrostatic interactions alchVdwLambdaEnd sets the value of A above which all vdW interactions are fully enabled for exnihilated particles For an exnihilated particle vdW interactions are fully decoupled at A 0 The coupling of vdW interactions to the simulation is then increased with increasing values of A such that at values of A greater than or equal to alchVdwLambdaEnd the vdW interactions of the exnihilated particle are fully coupled to the simulation 170 For an annihilated particle vdW interactions are completely coupled to the simulation for A values between 0 and 1 alchVdwLambdaEnd Then vdW interactions of the annihilated particle are linearly decoupled over the range of A value
150. eField may return yes and 1 2 3 before the first run command but 1 and 1 0 2 0 3 0 after parsing istrue eFieldOn would return 1 in both cases Similarly isset badparam will return 0 before parsing but raise an unknown parameter error after 6 Between run commands the reassignTemp rescaleTemp and langevinTemp parame ters can be changed to allow simulated annealing protocols within a single config file The useGroupPressure useFlexibleCell useConstantArea useConstantRatio LangevinPis ton LangevinPistonTarget LangevinPistonPeriod LangevinPistonDecay LangevinPiston Temp SurfaceTensionTarget BerendsenPressure BerendsenPressureTarget BerendsenPres sureCompressibility and BerendsenPressureRelaxationTime parameters may be changed to allow pressure equilibration The fixedAtoms constraintScaling and nonbondedScaling pa rameters may be changed to preserve macromolecular conformation during minimization and equilibration fixedAtoms may only be disabled and requires that fixedAtomsForces is en abled to do this The consForceScaling parameter may be changed to vary steering forces or to implement a time varying electric field that affects specific atoms The eField eFieldFreq and eFieldPhase parameters may be changed to implement at time varying electric field that affects all atoms The alchLambda and alchLambda2 parameters may be changed during alchemical free energ
151. ear Bias Experiment Directed Simulation Experiment directed simulation applies a linear bias with a changing force constant Please cite White and Voth 76 when using this feature As opposed to that reference the force constant here is scaled by the width corresponding to the biased colvar In White and Voth each force constant is scaled by the colvars set center The bias converges to a linear bias after which it will be the minimal possible bias You may also stop the simulation take the median of the force constants ForceConst found in the colvars trajectory file and then apply a linear bias with that constant All the notes about units described in sections 10 5 4 and 10 5 3 apply here as well This is not a valid simulation of any particular statistical ensemble and is only an optimization algorithm until the bias has converged e centers lt Collective variable centers gt Context alb Acceptable Values space separated list of colvar values Description The desired center equilibrium values which will be sought during the adaptive linear biasing The number of values must be the number of requested colvars Each value is a decimal number if the corresponding colvar returns a scalar a x y z triplet if it returns a unit vector or a vector and a q0 q1 q2 q3 quadruplet if it returns a rotational quaternion If a colvar has periodicities or symmetries its closest image to the restraint center is considered when calcu
152. ect computation of electrostatics is not intended to be used during real calculations but rather as a testing or comparison measure Because of the O N computational complexity for performing direct calculations this is much slower than using PME or MSM to compute full electro statics for large systems In the case of periodic boundary conditions the nearest image convention is used rather than a full Ewald sum e FullDirect lt calculate full electrostatics directly gt Acceptable Values yes or no Default Value no Description Specifies whether or not direct computation of full electrostatics should be performed 5 2 7 Tabulated nonbonded interaction parameters In order to support coarse grained models and semiconductor force fields the tabulated energies feature replaces the normal van der Waals potential for specified pairs of atom types with one interpolated from user supplied energy tables The electrostatic potential is not altered Pairs of atom types to which the modified interactions apply are specified in a CHARMM parameter file by an NBTABLE section consisting of lines with two atom types and a corresponding interaction type name For example tabulated interactions for SI O O O and SI SI pairs would be specified in a parameter file as NBTABLE SI 0 SIO 0 0 00 SI SI SISI Each interaction type must correspond to an entry in the energy table file The table file consists of a header formatted as multiple commen
153. ect is faster conformational sampling to find minimum energy structures The method is implemented exactly as described by 177 Zhang and Ma in J Chem Phys 132 244101 2010 using Equation 18 of their paper to calculate the average energy at a given temperature from the histogram of energies The dynamic temperature is realized either by changing the temperature of the Langevin ther mostat or by velocity rescaling 12 2 1 NAMD parameters The following parameters are used to adaptive tempering e adaptTempMD lt Is adaptive tempering active gt Acceptable Values on or off Default Value off Description Specifies whether or not adaptive tempering is used If set to on then the following parameters are required to be set either all of adaptTempTmin adaptTempTmax adaptTempBins adaptTempDt or adaptTempInFile but not both e adaptTempFreq lt steps between temperature updates gt Acceptable Values Positive integers Default Value 10 Description The number of steps between temperature updates Note that the potential energy at the current is calculated and added to the temperature energy histogram at every step e adaptTempTmin lt minimum temperature K gt Acceptable Values Positive real number Description Sets the minimum temperature to be used in the simulation e adaptTempTmax lt maximum temperature K gt Acceptable Values Positive real number Description Sets the maximum temperature to be used in the
154. ectrostatic pairs will be directly calculated every timestep Outside of this distance interactions will be calculated only periodically These forces will be applied using a multiple timestep integration scheme as described in Section 7 3 4 5 2 3 Non bonded force field parameters e cutoff lt local interaction distance common to both electrostatic and van der Waals calcu lations A gt Acceptable Values positive decimal Description See Section 5 2 for more information 48 energy d cutoff distance Figure 2 Graph showing an electrostatic potential with and without the application of the shifting function gt direct at Bo every step S o cutoff 0 distance Figure 3 Graph showing an electrostatic potential when full electrostatics are used within NAMD with one curve portion calculated directly and the other calculated using PME e switching lt use switching function gt Acceptable Values on or off Default Value on Description If switching is specified to be off then a truncated cutoff is performed If switching is turned on then smoothing functions are applied to both the electrostatics and van der Waals forces For a complete description of the non bonded force parameters see Section 5 2 If switching is set to on then switchdist must also be defined e vdwForceSwitching lt use force switching for VDW gt Acceptable Values on or off Default Value off Descri
155. ecular systems Theoretical and experimental applications pages 27 59 Escom The Netherlands 1989 Y Wang C Harrison K Schulten and J McCammon Implementation of accelerated molec ular dynamics in NAMD Comp Sci Discov 4 015002 2011 J Weiser P Senkin and W C Still Approximate atomic surfaces from linear combinations of pairwise overlaps LCPO J Comp Chem 20 217 230 1999 A D White and G A Voth Efficient and minimal method to bias molecular simulations with experimental data J Chem Theory Comput ASAP 2014 P C Whitford J K Noel S Gosavi A Schug K Y Sanbonmatsu and J N Onuchic An all atom structure based potential for proteins Bridging minimal models with all atom empirical forcefields 75 2 430 441 2009 217 78 P C Whitford A Schug J Saunders S P Hennelly J N Onuchic and K Y Sanbonmatsu Nonlocal helix formation is key to understanding s adenosylmethionine 1 riboswitch function Biophysical Journal 96 2 L7 L9 2009 79 R W Zwanzig High temperature equation of state by a perturbation method i nonpolar gases J Chem Phys 22 1420 1426 1954 218 Index 1 4scaling parameter 50 abort command 18 accelMD parameter 176 accelMDalpha parameter 176 accelMDdihe parameter 176 accelMDdual parameter 176 accelMDE parameter 176 accelMDFirstStep parameter 177 accelMDLastStep parameter 177 accelMDOutFreq parameter 177 accelMDTalpha paramete
156. ed by scriptedFunctionVectorSize Non scalar values should be passed as space separated lists e g 1 2 3 e scriptedFunctionVectorSize lt Dimension of the vector value of a scripted colvar gt Context colvar Acceptable Values positive integer Description This parameter is only valid when scriptedFunctionType is set to vector It defines the vector length of the colvar value returned by the function 10 5 Biasing and analysis methods All of the biasing and analysis methods implemented abf harmonic histogram and metadynamics recognize the following options e name lt Identifier for the bias gt Context colvar bias Acceptable Values string Default Value lt type of bias gt lt bias index gt Description This string is used to identify the bias or analysis method in output messages and to name some output files e colvars lt Collective variables involved gt Context colvar bias Acceptable Values space separated list of colvar names Description This option selects by name all the colvars to which this bias or analysis will be applied e outputEnergy lt Write the current bias energy to the trajectory file gt Context colvar bias Acceptable Values boolean Default Value off 146 Description If this option is chosen and colvarsTrajFrequency is not zero the current value of the biasing energy will be written to the trajectory file during the simulation 10 5 1 Adaptive Biasing Force For a full de
157. ed minimization along the same directions Along each direction a minimum is first bracketed rigorously bounded and then converged upon by either a golden section search or when possible a quadratically convergent method using gradient information For most systems it just works e minimization lt Perform conjugate gradient energy minimization gt Acceptable Values on or off Default Value off Description Turns efficient energy minimization on or off e minTinyStep lt first initial step for line minimizer gt Acceptable Values positive decimal Default Value 1 0e 6 Description If your minimization is immediately unstable make this smaller e minBabyStep lt max initial step for line minimizer gt Acceptable Values positive decimal Default Value 1 0e 2 Description If your minimization becomes unstable later make this smaller e minLineGoal lt gradient reduction factor for line minimizer gt Acceptable Values positive decimal Default Value 1 0e 4 Description Varying this might improve conjugate gradient performance 7 2 2 Velocity quenching parameters You can perform energy minimization using a simple quenching scheme While this algorithm is not the most rapidly convergent it is sufficient for most applications There are only two parameters for minimization one to activate minimization and another to specify the maximum movement of any atom e velocityQuenching lt Perform old style energy minimization
158. ee Eee 109 9 12 External Program Forces oaoa 112 10 Collective Variable based Calculations 113 10 1 General parameters and input output files 113 10 1 1 NAMD parameters said ada oa Ae a y Ae ee RO eg 113 10 1 2 Configuration syntax for the collective variables module 115 10 1 3 Input state file optional Laa A ene ey Ea 118 101 4 Output Blest aa di a a a a a 118 10 2 Defining collective variables and their properties o 118 10 2 1 General options for a collective variable 119 10 2 2 Artificial boundary potentials wallS hs EA A 120 102 3 Traject ry OU DIN sce ce a dl a a ee ede ee ene Gh ee 121 10 2 4 Extended Lagrangian 0 000 eee ee 122 10 2 5 Statistical analysis of collective variables 0 0 0 200004 123 10 3 Selecting atoms for colvars defining atom groups 2 0208 125 10 3 1 Selection keywords ee 125 10 3 2 Moving frame of reference e 127 10 3 3 Treatment of periodic boundary conditions o soo 129 10 3 4 Computational cost of colvars based on group size ooo a a 130 10 4 Collective variable components basis functions 004 130 10 4 1 List of available colvar components s oao a 00 eee eee 131 10 4 2 Advanced usage and special considerations o o sooo a 005 143 10 4 3 Linear and polynomial combinations of components 145 10 4 4 Col
159. een the initial and the final states see Figure 8 11 1 3 Thermodynamic Integration An alternative to the perturbation formula for free energy calculation is Thermodynamic Integration TI With the TI method the free energy is given as 40 69 24 aa UE ay 61 In the multi configuration thermodynamic integration approach 69 implemented in NAMD OH x Px A OA the ensemble average of the derivative of the internal energy with respect to A 167 is collected for a series of discrete values and written to tilutFile These values are analyzed by the separately distributed script NAMD_ti pl which performs the integration of individual energy components and reports back the total AA values for the transformation 11 2 Implementation of the free energy methods in NAMD The procedures implemented in NAMD are particularly adapted for performing free energy cal culations that split the A reaction path into a number of non physical intermediate states or windows Separate simulations can be started for each window Alternatively the TCL scripting ability of NAMD can be employed advantageously to perform the complete simulation in a single run An example making use of such a script is supplied at the end of this section The following keywords can be used to run alchemical free energy calculations whether FEP or TI e alch lt Is an alchemical transformation to be performed gt Acceptable Values on or off Defaul
160. elojes Arise P75 007s 1 Pio g 2070 2r2 po rij ojs ri Tij pjs 2 2 vol pis ri s 1 Ip Pisa his 2 2 oa 3 2 rlr 2rij Tig TPis VI Other variables referenced in the above GB equations are rij distance between atoms i and j calculated from atom coordinates k debye screening length calculated from ion concentration k 4 ete KT 10 for 0 1 M monovalent salt s dielectric constant of solvent p dielectric constant of protein a Born radius of atom 7 pi intrinsic radius of atom i taken from Bondi 9 po intrinsic radius offset p 0 09 A by default 56 Pio Pi PO Pis Pio Sij Sij atom radius scaling factor 33 67 ke Coulomb s constant 332 063711 kcal A e reo 16 B y 0 8 0 2 91 or 1 0 0 8 4 85 56 6 2 3 Phase Calculation The GBIS algorithm requires three phases of calculation with each phase containing an iteration over all atom pairs with the cutoff In phase 1 the screening of atom pairs is summed at the 2 OEG eer conclusion of phase 1 the Born radii are calculated In phase 2 the Pi force contribution hereafter called the dEdr force is calculated as well as the partial derivative of the Born radii with GB respect to the atom positions A In phase 3 the a dre force contribution hereafter called the dEda force is calculated 69 6 3 Configuration Parameters When using GBIS user s should not u
161. en the gradient estimate has a large variance See the fullSamples parameter below for details As sampling of the phase space proceeds the estimate V A is progressively refined The biasing force introduced in the equations of motion guarantees that in the bin centered around the forces acting along the selected collective variables average to zero over time Eventually as the undelying free energy surface is canceled by the adaptive bias evolution of the system along is governed mainly by diffusion Although this implementation of ABF can in principle be used in arbitrary dimension a higher dimension collective variable space is likely to result in sampling difficulties Most commonly the number of variables is one or two ABF requirements on collective variables 1 Only linear combinations of colvar components can be used in ABF calculations 2 Availability of system forces is necessary The following colvar components can be used in ABF calculations distance distance_xy distance_z angle dihedral gyration rmsd and eigenvector Atom groups may not be replaced by dummy atoms unless they are excluded from the force measurement by specifying oneSiteSystemForce if available 3 Mutual orthogonality of colvars In a multidimensional ABF calculation equation 51 must be satisfied for any two colvars and Various cases fulfill this orthogonality condition e and are based on non overlapping sets of atoms e
162. ended for testing purposes and should not be used in routine simulations e updateBias lt Update the ABF bias gt Context abf Acceptable Values boolean Default Value yes Description If this is set to no the initial biasing force e g read from a restart file or through inputPrefix is not updated during the simulation As a result a constant bias is applied This can be used to apply a custom tabulated biasing potential to any combination of colvars To that effect one should prepare a gradient file containing the gradient of the potential to be applied negative of the bias force and a count file containing only values greater than fullSamples These files must match the grid parameters of the colvars Multiple replica ABF e shared lt Apply multiple replica ABF sharing force samples among the replicas gt Context abf Acceptable Values boolean Default Value no Description This is command requires that NAMD be compiled and executed with 150 multiple replica support If shared is set to yes the system force samples will be synchronized among all replicas at intervals defined by sharedFreq Thus it is as if system force samples among all replicas are gathered in a single shared buffer which why the algorithm is referred to as shared ABF Shared ABF allows all replicas to benefit from the sampling done by other replicas and can lead to faster convergence of the biasing force e sharedFreq lt Frequency in timesteps
163. eptable Values positive integer Description Specifies the index of the last ligand atom 185 e ramd ramdSeed lt Set RAMD seed gt Acceptable Values positive integer Default Value 14253 Description Specifies seed for the random number generator for generation of acceleration directions Change this parameter if you wish to run different trajectories with identical parameters Note In combined RAMD MD simulations RAMD blocks alternate with standard MD blocks ramdSteps and mdSteps input parameters The switches between RAMD and MD blocks are decided based on the following parameters i d the distance between the protein and ligand centers of mass ii dr the distance traveled by the ligand in 1 RAMD block and iii dm the distance traveled by the ligand in 1 MD block A switch from RAMD to MD is applied if dr gt rRamdMin A switch from MD to RAMD is applied if i dm lt rMdMin and d gt 0 acceleration direction is kept from previous RAMD block ii if dm lt rMdMiv and d lt 0 acceleration direction is changed iii if dm gt rMdMin and d lt 0 acceleration direction is changed In all other case a switch is not applied 186 13 Structure based simulations 13 1 Hybrid MD Go Simulation 13 1 1 Hybrid MD Go model NAMD incorporates a hybrid MD Go model hereby referred to as Go to study the conformation changes in biomolecular
164. er a run or minimize statement Collective variables and biases can be added queried and deleted through the scripting com mand cv with the following syntax cv lt subcommand gt largs For example to query the value of a collective variable named myVar use the following syntax set value cv colvar myVar value All subcommands of cv are documented below 10 6 1 Managing the colvars module e configfile lt file name gt read configuration from a file e config lt string gt read configuration from the given string both config and configfile subcommands may be invoked multiple times e reset delete all internal configuration of the colvars module e version return the version of the colvars code 10 6 2 Input and output e list return a list of all currently defined variables 163 list biases return a list of all currently defined biases i e sampling and analysis algo rithms load lt file name gt load a collective variables state file typically produced during a simula tion save lt prefiz gt save the current state in a file whose name begins with the given argument if any of the biases have additional output files defined those are saved as well update recalculate all colvars and biases based on the current atomic coordinates printframe return a summary of the current frame in a format equivalent to a line of the collective variables trajectory file printframelabels return text labels
165. er they are numbered by the operating system This may not be the fastest configuration if NAMD is running fewer threads than there are cores available and consecutively numbered cores share resources such as memory bandwidth or are hardware threads on the same physical core If needed specific cores for the Charm PEs processing elements and communication threads on all SMP builds and on multicore builds when the commthread option is specified can be set by adding the pemap and if needed commap options with lists of core sets in the form lower upper stride run A single number identifies a particular core Two numbers separated by a dash identify an inclusive range lower bound and upper bound If they are followed by a colon and another number a stride that range will be stepped through in increments of the additional number Within each stride a dot followed by a run will indicate how many cores to use from that starting point For example the sequence 0 8 2 16 20 24 includes cores 0 2 4 6 8 16 20 21 22 23 24 On a 4 way quad core system three cores from each socket would be 0 15 4 3 if cores on the same chip are numbered consecutively There is no need to repeat cores for each node in a run as they are reused in order For example the IBM POWER7 has four hardware threads per core and the first thread can use all of the core s resources if the other threads are idle threads 0 and 1 split the core if threads
166. ere 8 is the compressibility which is RMS of roughly 100 bar for a 10 000 atom biomolecular system Much larger fluctuations are regularly observed in practice The instantaneous pressure for a biomolecular system is well defined for internal forces that are based on particular periodic images of the interacting atoms conserve momentum and are translationally invariant When dealing with externally applied forces such as harmonic constraints fixed atoms and various steering forces NAMD bases its pressure calculation on the relative 83 positions of the affected atoms in the input coordinates and assumes that the net force will average to zero over time For time periods during with the net force is non zero the calculated pressure fluctuations will include a term proportional to the distance to the affected from the user defined cell origin A good way to observe these effects and to confirm that pressure for external forces is handled reasonably is to run a constant volume cutoff simulation in a cell that is larger than the molecular system by at least the cutoff distance the pressure for this isolated system should average to zero over time Because NAMD s impluse basd multiple timestepping system alters the balance between bonded and non bonded forces from every timestep to an average balance over two steps the calculated pressure on even and odd steps will be different The PRESSAVG and GPRESSAVG fields provide the average over the no
167. ered and synchronized with the disk only when the restart file is being written e colvarsTrajAppend lt Append to trajectory file gt Context global Acceptable Values boolean Default Value off Description If this flag is enabled and a file with the same name as the trajectory file is already present new data is appended to that file Otherwise a new file is created with the same name that overwrites the previous file Note when running consecutive simulations with the same outputName e g in FEP calculations you should enable this option to preserve the previous contents of the trajectory file e colvarsRestartFrequency lt Colvar module restart frequency gt Context global Acceptable Values positive integer Default Value restartFreq Description Allows to choose a different restart frequency for the collective variables module Redefining it may be useful to trace the time evolution of those few properties which are not written to the trajectory file for reasons of disk space e indexFile lt Index file for atom selection GROMACS ndx format gt Context global Acceptable Values UNIX filename Description This option reads an index file usually with a ndx extension as produced by the make_ndx tool of GROMACS This keyword may be repeated to load multiple index files the same group name cannot appear in multiple index files The names of index groups contained in this file can then be used to define atom groups w
168. ergy contribution from implicit solvent is calculated it is proportional to the solvent accessible surface area SASA which is calculated by the Linear Combination of Pairwise Overlap LCPO method 75 It evaluated every nonbondedFreq steps and its energy is added into the reported ELECT energy e surfaceTension lt surface tension of SASA energy gt Acceptable Values positive decimal Default Value 0 005 kcal mol A Description Surface tension used when calculating hydrophobic SASA energy Enonpolar surface Tension x surfaceArea Below is a sample excerpt from a NAMD config file for nonbonded and multistep parameters when using GBIS and SASA GBIS parameters GBIS on ionConcentration 0 3 alphaCutoff 14 nonbonded parameters switching on switchdist 15 cutoff 16 pairlistdist 18 hydrophobic energy sasa on surfaceTension 0 006 multistep parameters timestep 1 nonbondedFreq 2 fullElectFrequency 4 71 7 Standard Minimization and Dynamics Parameters 7 1 Boundary Conditions In addition to periodic boundary conditions NAMD provides spherical and cylindrical boundary potentials to contain atoms in a given volume To apply more general boundary potentials written in Tcl use tc1BC as described in Sec 9 11 7 1 1 Periodic boundary conditions NAMD provides periodic boundary conditions in 1 2 or 3 dimensions The following parameters are used to define these boundary conditions e cellBasisVector1 lt basis vector for
169. es boolean Default Value off Description If this option is on the center of geometry of the group will be aligned with that of the reference positions provided by either refPositions or refPositionsFile Colvar components will only have access to the aligned positions Note unless otherwise specified rmsd and eigenvector set this option to on by default e rotateReference lt Implicitly remove rotations for this group gt Context atom group Acceptable Values boolean Default Value off Description If this option is on the coordinates of this group will be optimally superim posed to the reference positions provided by either refPositions or refPositionsFile The rotation will be performed around the center of geometry if centerReference is on around the origin otherwise The algorithm used is the same employed by the orientation colvar component 19 Forces applied to the atoms of this group will also be implicitly rotated back to the original frame Note unless otherwise specified rmsd and eigenvector set this option to on by default e refPositions lt Reference positions for fitting A gt Context atom group Acceptable Values space separated list of x y z triplets 127 Description This option provides a list of reference coordinates for centerReference or rotateReference If only centerReference is on the list may contain a single x y z triplet if also rotateReference is on the list should be as long as the atom
170. es whether or not the MARTINI forcefield is being used specifically cosine based angle potential function The cosine based potential will only be used for angles in CHARMM parameter files that specify the cos keyword e martiniSwitching lt enable the MARTINI Lennard Jones switching function gt Acceptable Values on or off Default Value off Description Specifies whether or not the MARTINI forcefield is being used specifically the Lennard Jones switching function e martiniDielAllow lt Allow dielectrics 15 0 for use with MARTINI gt Acceptable Values on or off Description off Allows user to specify a dielectric not equal to 15 0 ie a non standard dielectric for MARTINI 5 6 Constraints and Restraints 5 6 1 Bond constraint parameters e rigidBonds lt controls if and how ShakeH is used gt Acceptable Values none water all Default Value none Description When water is selected the hydrogen oxygen and hydrogen hydrogen dis tances in waters are constrained to the nominal length or angle given in the parameter file making the molecules completely rigid When rigidBonds is all waters are made rigid as described above and the bond between each hydrogen and the one atom to which it is bonded is similarly constrained For the default case none no lengths are constrained e rigidTolerance lt allowable bond length error for ShakeH A gt Acceptable Values positive decimal Default Value 1 0e 8 Description The ShakeH a
171. esses are attempted based on bond lengths of 1 A and angles of 109 Arguments None Context After stucture has been generated and known coordinates read in writepdb lt file name gt Purpose Writes PDB file containing coordinates Atom order is identical to PSF file gener ated by writepsf unless structure has been changed The O field is set to 1 for atoms with known coordinates 0 for atoms with guessed coordinates and 1 for atoms with no coordinate data available coordinates are set to 0 for these atoms Arguments lt file name gt PDB file to be written Context After structure and coordinates are complete 44 e writenamdbin lt file name gt velnamdbin velocity file name Purpose Writes NAMD binary file containing coordinates Atom order is identical to PSF file generated by writepsf unless structure has been changed Coordinates are set to 0 for atoms with no coordinate data Arguments lt file name gt NAMD binary file to be written velnamdbin Also write velocities to NAMD binary file lt velocity file name gt NAMD binary velocity file to be written Context After structure and coordinates are complete 4 5 Example of a Session Log The command writepsf prints a simple session log as REMARKS at the beginning of the PSF file The log contains information about applied patches and used topology files which not stored in the standard records of PSF files These informations are also available afte
172. et threshold for distance traveled in MD gt Acceptable Values positive decimal Description Specifies a threshold value for the distance in Angstroms traveled by accel erated atoms in 1 standard MD block In combined RAMD MD simulations a switch from a standard MD block to a RAMD block is applied according to the criteria described in the note below Required if mdStep is not 0 ignored if mdSteps is 0 ramd forceQutFreq lt Set frequency of RAMD forces output gt Acceptable Values positive integer Must be divisor of both ramdSteps and mdSteps Default Value 0 Description Every forceOutFreq steps detailed output of forces will be written ramd maxDist lt Set center of mass separation gt Acceptable Values positive decimal Default Value 50 Description Specifies the distance in Angstroms between the the centers of mass of the ligand and the protein when the simulation is stopped ramd firstProtAtom lt First index of protein atom gt Acceptable Values positive integer Default Value 1 Description Specifies the index of the first protein atom ramd lastProtAtom lt Last index of protein atom gt Acceptable Values positive atom Description Specifies the index of the last protein atom ramd firstRamdAtom lt First index of ligand atom gt Acceptable Values positive integer Description Specifies the index of the first ligand atom ramd lastRamdAtom lt Last index of ligand atom gt Acc
173. eter 55 MTSAlgorithm parameter 79 multipleReplicas colvars metadynamics key word 155 multiply psfgen command 41 mutate psfgen command 41 myReplica command 19 name colvars colvar keyword 119 name colvars metadynamics keyword 156 name colvars colvar bias keyword 146 newHillFrequency colvars metadynamics key word 153 nonbondedFreq parameter 79 nonbondedScaling parameter 17 50 numNodes command 18 numPes command 18 numPhysicalNodes command 18 numReplicas command 19 numsteps parameter 76 oneSiteSystemForce colvars angle dihedral keyword 134 oneSiteSystemForce colvars distanceZ distanceXY keyword 133 oneSiteSystemForce colvars distance key word 132 OPLS 51 output command 17 output onlyforces command 17 output withforces command 17 outputAccumulatedWork colvars harmonic keyword 159 outputAppliedForce colvars colvar keyword 121 outputCenters colvars harmonic keyword 158 outputEnergies parameter 27 outputEnergy colvars colvar keyword 121 outputEnergy colvars colvar bias keyword 146 outputFreq colvars abf keyword 149 outputFreq colvars histogram keyword 162 outputMomenta parameter 27 outputname parameter 24 outputPairlists parameter 91 outputPressure parameter 27 outputSystemForce colvars colvar keyword 121 outputTiming parameter 27 223 outputValue colvars colvar keyword 121 output Velocity colvars colvar keyword 121 pairInteraction parame
174. ew the current state of the system or perform interactive steering 104 e IMDon lt is IMD active gt Acceptable Values on or off Default Value off Description Specifies whether or not to listen for an IMD connection e IMDport lt port number to expect a connection on gt Acceptable Values positive integer Description This is a free port number on the machine that node 0 is running on This number will have to be entered into VMD e IMDfreq lt timesteps between sending coordinates gt Acceptable Values positive integer Description This allows coordinates to be sent less often which may increase NAMD performance or be necessary due to a slow network e IMDwait lt wait for an IMD connection gt Acceptable Values yes or no Default Value no Description If no NAMD will proceed with calculations whether a connection is present or not If yes NAMD will pause at startup until a connection is made and pause when the connection is lost e IMDignore lt ignore interactive steering forces gt Acceptable Values yes or no Default Value no Description If yes NAMD will ignore any steering forces generated by VMD to allow a simulation to be monitored without the possibility of perturbing it 9 10 Tcl Forces and Analysis NAMD provides a limited Tcl scripting interface designed for applying forces and performing on the fly analysis This interface is efficient if only a few coordinates either of individual atoms or
175. eyword 142 hBondCutoff colvars alpha keyword 142 hBondExpDenom colvars alpha keyword 142 hBondExpNumer colvars alpha keyword 142 hgroupCutoff A parameter 90 hideJacobian colvars abf keyword 149 hillWeight colvars metadynamics keyword 153 hillWidth colvars metadynamics keyword 154 historyFreq colvars abf keyword 150 IMDfreq parameter 105 IMDignore parameter 105 IMDon parameter 105 IMDport parameter 105 IMDwait parameter 105 indexFile colvars global keyword 116 indexGroup colvars atom group keyword 126 inputPrefix colvars abf keyword 150 intrinsicRadiusOffset parameter 70 ionConcentration parameter 70 isset command 17 istrue command 17 keepHills colvars metadynamics keyword 157 lambdaSchedule colvars harmonic keyword 160 langevin parameter 80 langevinCol parameter 81 langevinDamping parameter 80 langevinFile parameter 80 langevinHydrogen parameter 80 LangevinPiston parameter 17 86 LangevinPistonDecay parameter 17 86 LangevinPistonPeriod parameter 17 86 LangevinPistonTarget parameter 17 86 LangevinPistonTemp parameter 17 87 langevinTemp parameter 17 80 last psfgen command 40 les parameter 180 lesCol parameter 181 lesFactor parameter 180 lesFile parameter 181 lesReduceMass parameter 181 lesReduceTemp parameter 180 limitdist parameter 51 LJcorrection parameter 51 longSplitting parameter 79 loweAndersen parameter 83 loweAndersenCutoff para
176. f possible values of each component in a given simulation and make use of wrapAround to limit this problem whenever possible Non scalar components When one of the following components are used the defined colvar returns a value that is not a scalar number e distanceVec 3 dimensional vector of the distance between two groups e distanceDir 3 dimensional unit vector of the distance between two groups e orientation 4 dimensional unit quaternion representing the best fit rotation from a set of reference coordinates The distance between two 3 dimensional unit vectors is computed as the angle between them The distance between two quaternions is computed as the angle between the two 4 dimensional unit vectors because the orientation represented by q is the same as the one represented by q distances between two quaternions are computed considering the closest of the two symmetric images Non scalar components carry the following restrictions e Calculation of system forces outputSystemForce option is currently not implemented e Each colvar can only contain one non scalar component e Binning on a grid abf histogram and metadynamics with useGrids enabled is currently not implemented for colvars based on such components Note while these restrictions apply to individual colvars based on non scalar components no limit is set to the number of scalar colvars To compute multi dimensional histograms and PMFs use sets of scalar c
177. f processors that a run must use before pairlists will be enabled on fewer processors small local pairlists are generated and recycled rather than being saved the default is pairlistMinProcs 1 This is a per simulation rather than a compile time option because memory usage is molecule dependent Additional information on reducing memory usage may be found at http www ks uiuc edu Research namd wiki index cgi NamdMemoryReduction 209 17 13 Improving Parallel Scaling While NAMD is designed to be a scalable program particularly for simulations of 100 000 atoms or more at some point adding additional processors to a simulation will provide little or no extra performance If you are lucky enough to have access to a parallel machine you should measure NAMD s parallel speedup for a variety of processor counts when running your particular simulation The easiest and most accurate way to do this is to look at the Benchmark time lines that are printed after 20 and 25 cycles usually less than 500 steps You can monitor performance during the entire simulation by adding output Timing steps to your configuration file but be careful to look at the wall time rather than CPU time fields on the TIMING output lines produced For an external measure of performance you should run simulations of both 25 and 50 cycles see the stepspercycle parameter and base your estimate on the additional time needed for the longer simu
178. f the water in watpsf is QQQ We want to delete waters outside of a box ten Angstroms bigger than the extent of the protein set protein atomselect top not segid QQQ set minmax measure minmax protein foreach min max minmax break foreach xmin ymin zmin min break foreach xmax ymax zmax max break set xmin expr xmin 10 set ymin expr ymin 10 set zmin expr zmin 10 set xmax expr xmax 10 set ymax expr ymax 10 set zmax expr zmax 10 Center the water on the protein Also update the coordinates held by psfgen set wat atomselect top segid QQQ wat moveby vecsub measure center protein measure center wat foreach atom wat get segid resid name x y z foreach segid resid name x y z atom break coord segid resid name list x y z Select waters that we don t want in the final structure set outsidebox atomselect top segid QQQ and x lt xmin or y lt ymin or z lt zmin or x gt xmax or y gt ymax or z gt xmax 38 set overlap atomselect top segid QQQ and within 2 4 of not segid QQQ Get a list of all the residues that are in the two selections and delete those residues from the structure set reslist concat outsidebox get resid overlap get resid set reslist lsort unique integer reslist foreach resid reslist delatom QQQ resid That should do it write out the new psf and pdb file write
179. fault format required by NAMD cmap Write cross term entries to PSF file if present the default nocmap Do not write cross term entries to PSF file even if present lt file name gt PSF file to be generated Context After all segments have been built and patched readpsf lt file name gt pdb pdb file name namdbin namdbin file name velnamdbin velocity file name Purpose Read in structure information from PSF file and add it to the structure Option ally also read coordinates and insertion codes from a PDB file assuming that the atom order is the same in both files Optionally also read coordinates a NAMD binary file assuming that the atom order is the same as the psf file It is an error if any segments in the PSF file already exist Arguments lt file name gt PSF file in X PLOR format names for atom types 43 pdb Read coordinates and insertion codes from PDB file lt pdb file name gt PDB file with atoms in same order as PSF file namdbin Read coordinates from NAMD binary file lt namdbin file name gt NAMD binary file with atoms in same order as PSF file velnamdbin Read velocities from NAMD binary file lt velocity file name gt NAMD binary velocity file with atoms in same order as PSF file Context Anywhere but within segment pdbalias atom lt residue name gt lt alternate name gt lt real name gt Purpose Provide translations from atom names found in PDB files to proper atom names read in f
180. fficients gt Acceptable Values X Y Z 0 or B Default Value 0 Description Column of the PDB file to use for the temperature coupling coefficient for each atom This value can be read from any floating point column of the PDB file A value of 0 indicates that the atom will remain unaffected 7 4 3 Temperature rescaling parameters NAMD allows equilibration of a system by means of temperature rescaling Using this method all of the velocities in the system are periodically rescaled so that the entire system is set to the desired temperature The following parameters specify how often and to what temperature this rescaling is performed 81 e rescaleFreq lt number of timesteps between temperature rescaling gt Acceptable Values positive integer Description The equilibration feature of NAMD is activated by specifying the number of timesteps between each temperature rescaling If this value is given then the rescaleTemp parameter must also be given to specify the target temperature e rescaleTemp lt temperature for equilibration K gt Acceptable Values positive decimal Description The temperature to which all velocities will be rescaled every rescaleFreq timesteps This parameter is valid only if rescaleFreq has been set 7 4 4 Temperature reassignment parameters NAMD allows equilibration of a system by means of temperature reassignment Using this method all of the velocities in the system are periodically reassigned so tha
181. field The Drude oscillators differ from typical spring bonds only in that they have an equilibrium length of zero The Drude oscillators are optionally supplemented by a maximal bond length parameter beyond which a quartic restraining potential is also applied The force field is also extended by an anisotropic spring term that accounts for out of plane forces from a polarized atom and its covalently bonded neighbor with two more covalently bonded neighbors similar in structure to an improper bond The screened Coulomb correction of Thole is calculated between pairs of Drude oscillators that would otherwise be excluded from nonbonded interaction and optionally between non excluded nonbonded pairs of Drude oscillators that are within a prescribed cutoff distance 71 72 Also included in the Drude force field are the use of off centered massless interaction sites so called lone pairs LPs to avoid the limitations of centrosymmetric based Coulomb in teractions 31 The coordinate of each LP site is constructed based on three guide atoms The calculated forces on the massless LP must be transferred to the guide atoms preserving 58 total force and torque After an integration step of velocities and positions the position of the LP is updated based on the three guide atoms along with additional geometry parame ters that give displacement and in plane and out of plane angles See our research web page http www ks uiuc edu Resear
182. for Langevin piston method This should be set equal to the target temperature for the chosen method of temperature control SurfaceTensionTarget lt Surface tension target dyn cm gt Acceptable Values decimal Default Value 0 0 Description Specifies surface tension target Must be used with useFlexibleCell and periodic boundary conditions The pressure specified in LangevinPistonTarget becomes the pressure along the z axis and surface tension is applied in the x y plane StrainRate lt initial strain rate gt Acceptable Values decimal triple x y z Default Value 0 0 0 Description Optionally specifies the initial strain rate for pressure control Is overridden by value read from file specified with extendedSystem There is typically no reason to set this parameter ExcludeFromPressure lt Should some atoms be excluded from pressure rescaling gt Acceptable Values on or off Default Value off Description Specifies whether or not to exclude some atoms from pressure rescaling The coordinates and velocites of such atoms are not rescaled during constant pressure simulations though they do contribute to the virial calculation May be useful for membrane protein simulation EXPERIMENTAL ExcludeFromPressureFile lt File specifying excluded atoms gt Acceptable Values PDB file Default Value coordinates file Description PDB file with one column specifying which atoms to exclude from pressure rescaling Specify 1 f
183. for the columns of printframe s output 10 6 3 Accessing collective variables colvar lt name gt value return the current value of colvar lt name gt colvar lt name gt update recalculate colvar lt name gt colvar lt name gt type return the type of colvar lt name gt colvar lt name gt delete delete colvar lt name gt colvar lt name gt addforce lt F gt apply given force on colvar lt name gt colvar lt name gt getconfig return config string of colvar lt name gt colvar lt name gt cvcflags lt flags gt for a colvar with several cvcs numbered according to their name string order set which cvcs are enabled or disabled in subsequent evaluations according to a list of 0 1 flags one per evc 10 6 4 Accessing biases bias lt name gt energy return the current energy of the bias lt name gt bias lt name gt update recalculate the bias lt name gt bias lt name gt delete delete the bias lt name gt bias lt name gt getconfig return config string of bias lt name gt 164 11 Alchemical Free Energy Methods Alchemical free energy calculations model the physically impossible but computationally realizable process of gradually mutating a subset of atoms of a system from one state to another through a series of intermediate steps Two alternative methods for alchemical calculation of free energies from molecular dynamics simulation are available in NAMD Free energy perturbation FEP and thermody
184. formats Descriptions of the output files formats are also given in Section 3 1 3 1 File formats 3 1 1 PDB files The PDB Protein Data Bank format is used for coordinate velocity force or other data being read or written by NAMD This is the standard format for coordinate data for most other molecular dynamics programs as well including X PLOR and CHARMM A full description of this file format can be obtained from the PDB web site at http www rcsb org pdb Positions in PDB files are stored in A Velocities in PDB files are stored in A ps and may be divided by PDBVELFAC TOR 20 45482706 to convert to the NAMD internal units used in DCD and NAMD binary files Forces in PDB files are stored in kcal mol A NAMD binary files below should be preferred to PDB files in most cases due to their higher precision 3 1 2 X PLOR format PSF files NAMD uses the same protein structure files that X PLOR does These files may be generated with psfgen VMD X PLOR or CHARMM CHARMM can generate an X PLOR format PSF file with the command write psf card xplor 3 1 3 CHARMM19 CHARMM22 and CHARMM27 parameter files NAMD supports CHARMM19 CHARMM22 and CHARMM27 parameter files in both X PLOR and CHARMM formats X PLOR format is the default CHARMM format parameter files may be used given the parameter paraTypeCharmm on For a full description of the format of commands used in these files see the X PLOR and CHARMM User s Manual 13 3
185. g is set by the width parameter see 10 2 1 The following specific parameters can be set in the ABF configuration block in addition to generic bias parameters such as colvars section 10 5 e fullSamples lt Number of samples in a bin prior to application of the ABF gt Context abf Acceptable Values positive integer Default Value 200 Description To avoid nonequilibrium effects due to large fluctuations of the force exerted along the colvars it is recommended to apply a biasing force only after a the estimate has started converging If fullSamples is non zero the applied biasing force is scaled by a factor a N between 0 and 1 If the number of samples N in the current bin is higher than fullSamples the factor is one If it is less than half of fullSamples the factor is zero and no bias is applied Between those two thresholds the factor follows a linear ramp from 0 to 1 a N 2NV fullSamples 1 e maxForce lt Maximum magnitude of the ABF force gt Context abf Acceptable Values positive decimals one per colvar Default Value disabled Description This option enforces a cap on the magnitude of the biasing force effectively applied by this ABF bias on each colvar This can be useful in the presence of singularities in the PMF such as hard walls where the discretization of the average force becomes very inaccurate causing the colvar s diffusion to get stuck at the singularity To enable this cap provide
186. gen command 42 psfcontext reset psfgen command 42 psfcontext stats psfgen command 43 psfSegID colvars alpha keyword 142 psfSegID colvars atom group keyword 126 ramd accel parameter 185 ramd debugLevel parameter 184 ramd firstProtAtom parameter 185 ramd firstRamdAtom parameter 185 ramd forceOutFreq parameter 185 ramd lastProtAtom parameter 185 ramd lastRamdAtom parameter 185 ramd maxDist parameter 185 ramd mdStart parameter 184 ramd mdSteps parameter 184 ramd ramdSeed parameter 186 ramd ramdSteps parameter 184 ramd rMinMd parameter 185 ramd rMinRamd parameter 185 rateMax colvars alb keyword 162 readexclusions parameter 28 readpsf psfgen command 43 reassignFreq parameter 82 reassignHold parameter 82 reassignIncr parameter 82 reassignTemp parameter 17 82 rebinGrids colvars metadynamics keyword 155 ref colvars distanceZ distanceXY keyword 132 ref2 colvars distanceZ distanceXY key word 132 refPositions colvars rmsd keyword 136 refPositions colvars atom group keyword 127 refPositionsCol colvars rmsd keyword 137 refPositionsCol colvars atom group keyword 128 refPositionsColValue colvars rmsd keyword 137 refPositionsCol Value colvars atom group key word 128 refPositionsFile colvars rmsd keyword 137 224 refPositionsFile colvars atom group keyword 128 refPositionsGroup colvars atom group key word 128 regenerate psfgen command 41 reinitatoms command 17 reinitvels co
187. grids Each subgrid spans a number of maingrid cells in each of the three dimensions and effectively redefines the data in that region The subgrids are usually defined at higher resolution with the restriction that the number of cells along each dimension is an integral number of the original number in the maingrid Note that the maingrid still has data points in regions where subgrids are defined and that on the boundary of a subgrid they must agree with the values in the subgrid Subgrids in turn may have subgrids of their own which may have subgrids of their own etc A non uniform grid file takes the form of a special comment block followed by multiple normal grid definitions The special comment block defines the grid hierarchy and consists of comments beginning with namdnugrid An example follows namdnugrid version 1 0 namdnugrid maingrid subgrids count 2 namdnugrid subgrid 1 generation 1 min x1 yl z1 max x2 y2 z2 subgrids count 2 namdnugrid subgrid 2 generation 2 min x3 y3 z3 max x4 y4 z4 subgrids count 0 namdnugrid subgrid 3 generation 2 min x5 y5 z5 max x6 y6 z6 subgrids count 0 namdnugrid subgrid 4 generation 1 min x7 y7 z7 max x8 y8 z8 subgrids count 0 HH HH HF HF The maingrid is described by the number of subgrids Subgrids are additionally described by a subgrid number a generation number which should be one higher than the generation of its super grid and min and max attributes which describe the location of the su
188. hange based on user feedback For this reason it is strongly recommended that forceDCDfreq be a multiple of fullElectFrequency 3 2 3 Standard output NAMD logs a variety of summary information to standard output The standard units used by NAMD are Angstroms for length kcal mol for energy Kelvin for temperature and bar for pressure Wallclock or CPU times are given in seconds unless otherwise noted 26 BOUNDARY energy is from spherical boundary conditions and harmonic restraints while MISC energy is from external electric fields and various steering forces TOTAL is the sum of the various potential energies and the KINETIC energy TOTAL2 uses a slightly different kinetic energy that is better conserved during equilibration in a constant energy ensemble TOTAL3 is another variation with much smaller short time fluctuations that is also adjusted to have the same running average as TOTAL2 Defects in constant energy simulations are much easier to spot in TOTAL3 than in TOTAL or TOTAL2 PRESSURE is the pressure calculated based on individual atoms while GPRESSURE incor porates hydrogen atoms into the heavier atoms to which they are bonded producing smaller fluc tuations The TEMPAVG PRESSAVG and GPRESSAVG are the average of temperature and pressure values since the previous ENERGY output for the first step in the simulation they will be identical to TEMP PRESSURE and GPRESSURE e outputEnergies lt timesteps between energy output gt
189. hanics of fluid mixtures J Chem Phys 3 300 313 1935 P A Kollman Free energy calculations Applications to chemical and biochemical phenomena Chem Rev 93 2395 2417 1993 E A Koopman and C P Lowe Advantages of a Lowe Andersen thermostat in molecular dynamics simulations J Chem Phys 124 204103 2006 A Laio and M Parrinello Escaping free energy minima Proc Natl Acad Sci USA 99 20 12562 12566 2002 G Lamoureux E Harder I V Vorobyov B Roux and A D MacKerell A polarizable model of water for molecular dynamics simulations of biomolecules Chem Phys Lett 418 1 3 245 249 2006 G Lamoureux and B Roux Modeling induced polarization with classical Drude oscillators Theory and molecular dynamics simulation algorithm J Chem Phys 119 6 3025 3039 2003 N Lu D A Kofke and T B Woolf Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods J Comput Chem 25 28 39 2004 Z M T P Straatsma and M J A Separation shifted scaling a new scaling method for Lennard Jones interactions in thermodynamic integration J Chem Phys 100 9025 9031 1994 215 48 51 52 53 54 57 58 59 60 61 62 A E Mark Free energy perturbation calculations In P v R Schleyer N L Allinger T Clark J Gasteiger P A Kollman H F Schaefer III and P R Schreiner editors Encyclopedi
190. hat each index is in use by only one replica at a time The keyword off will return to writing the local trajectory file set by the dedFile command 2 2 4 Required NAMD configuration parameters The following parameters are required for every NAMD simulation e numsteps page 77 e coordinates page 23 e structure page 23 e parameters page 23 e exclude page 50 e outputname page 24 e one of the following three temperature page 77 velocities page 24 binvelocities page 24 20 These required parameters specify the most basic properties of the simulation In addition it is highly recommended that pairlistdist be specified with a value at least one greater than cutoff 21 3 Input and Output Files NAMD was developed to be compatible with existing molecular dynamics packages especially the packages X PLOR 13 and CHARMM 12 To achieve this compatibility the set of input files which NAMD uses to define a molecular system are identical to the input files used by X PLOR and CHARMM Thus it is trivial to move an existing simulation from X PLOR or CHARMM to NAMD A description of these molecular system definition files is given in Section 3 1 In addition the output file formats used by NAMD were chosen to be compatible with X PLOR and CHARMM In this way the output from NAMD can be analyzed using X PLOR CHARMM or a variety of the other tools that have been developed for the existing output file
191. hat if Langevin dynamics are used in a parallel simulation i e a simulation using more than one processor even using the same seed will not guarantee reproducible results TT 7 3 3 Conserving momentum e zeroMomentum lt remove center of mass drift due to PME gt Acceptable Values yes or no Default Value no Description If enabled the net momentum of the simulation and any resultant drift is removed before every full electrostatics step This correction should conserve energy and have minimal impact on parallel scaling This feature should only be used for simulations that would conserve momentum except for the slight errors in PME Features such as fixed atoms harmonic restraints steering forces and Langevin dynamics do not conserve momentum use in combination with these features should be considered experimental Since the momentum correction is delayed enabling outputMomenta will show a slight nonzero linear momentum but there should be no center of mass drift 7 3 4 Multiple timestep parameters To further reduce the cost of computing full electrostatics NAMD uses a multiple timestepping integration scheme In this scheme the total force acting on each atom is broken into two pieces a quickly varying local component and a slower long range component The local force component is defined in terms of a splitting function The local force component consists of all bonded and van der Waals interactions as well as that portion of
192. he analysis of a DCD trajectory file using NAMD The file pair pdb contains the definition of pair interaction groups NAMD will compute the interaction energy and force between these groups for each frame in the DCD file It is assumed that coordinate frames were written every 1000 timesteps See Sec 14 1 for more about pair interaction calculations initial config coordinates alanin pdb temperature 0 output params outputname tmp alanin analyze binaryoutput no integrator params timestep 1 0 force field params structure alanin psf parameters alanin params exclude scaled1 4 1 4scaling 1 0 switching on switchdist 8 0 cutoff 12 0 pairlistdist 13 5 stepspercycle 20 Atoms in group 1 have a 1 in the B column group 2 has a 2 pairInteraction on pairInteractionFile pair pdb pairInteractionCol B pairInteractionGroup1 1 pairInteractionGroup2 2 First frame saved was frame 1000 set ts 1000 coorfile open dcd tmp alanin dcd Read all frames until nonzero is returned while coorfile read 4 Set firstTimestep so our energy output has the correct TS firstTimestep ts Compute energies and forces but don t try to move the atoms run 0 incr ts 1000 201 coorfile close 202 17 Running NAMD NAMD runs on a variety of serial and parallel platforms While it is trivial to launch a serial program a parallel program depends on a platform specific library such as MPI to launch copies
193. he cutoff so that pairs are allowed to move in and out of the cutoff distance without causing energy conservation to be disturbed also regenerate the patch grid In rare special circumstances atoms that are involved in bonded terms bonds angles dihedrals or impropers or nonbonded exclusions especially implicit exclusions due to bonds will be placed on non neighboring patches because they are more than the cutoff distance apart This can result in the simulation dying with a message of bad global exclusion count If an atoms moving too fast simulation has become unstable bad global exclusion count or similar error happens on the first timestep then there is likely something very wrong with the input coordinates such as the atoms with uninitialized coordinates or different atom orders in the PSF and PDB file Looking at the system in VMD will often reveal an abnormal structure Be aware that the atom IDs in the Atoms moving too fast error message are 1 based while VMD s atom indices are 0 based If an atoms moving too fast simulation has become unstable bad global exclusion count or similar error happens later in the simulation then the dynamics have probably become unstable resulting in the system exploding apart Energies printed at every timestep should show an exponential increase This may be due to a timestep that is too long or some other strange feature Saving a trajectory of every step an
194. he displayed force is the force on atoms in group 1 and is units of kcal mol For trajectory analysis the recommended way to use this set of options is to use the NAMD Tcl scripting interface as described in Sec 2 2 2 to run for O steps so that NAMD prints the energy without performing any dynamics e pairInteraction lt is pair interaction calculation active gt Acceptable Values on or off Default Value off Description Specifies whether pair interaction calculation is active e pairInteractionFile lt PDB file containing pair interaction flags gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to specify atoms to use for pair interaction calculations If this parameter is not specified then the PDB file containing initial coordinates specified by coordinates is used e pairInteractionCol lt column of PDB file containing pair interaction flags gt Acceptable Values X Y Z 0 or B Default Value B Description Column of the PDB file to specify which atoms to use for pair interaction calculations This parameter may specify any of the floating point fields of the PDB file either X Y Z occupancy or beta coupling temperature coupling e pairInteractionSelf lt compute within group interactions instead of bewteen groups gt Acceptable Values on or off Default Value off Description When active NAMD will compute bonded and nonbonded interactions only for atoms within group 1 e p
195. he same base options as the component orientation atoms and refPositions or refPositionsFile refPositionsCol and refPositionsColValue The returned value is the cosine of the angle of rotation 0 between the current and the reference positions The range of values is 1 1 spinAngle angle of rotation around a given axis The complete rotation described by orientation can optionally be decomposed into two sub rotations one is a spin rotation around e and the other a tilt rotation around an axis orthogonal to e The component spinAngle mea sures the angle of the spin sub rotation around e This can be defined using the same options as 140 the component orientation atoms and refPositions or refPositionsFile refPositionsCol and refPositionsColValue In addition spinAngle accepts the axis option e axis lt Special rotation axis A gt Context tilt spinAngle Acceptable Values x y z triplet Default Value 0 0 0 0 1 0 Description The three components of this vector define when normalized the special rotation axis used to calculate the tilt and spinAngle components The component spinAngle returns an angle in degrees within the periodic interval 180 180 Note the value of spinAngle is a continuous function almost everywhere with the exception of configurations with the corresponding tilt angle equal to 180 i e the tilt component is equal to 1 in those cases spinAngle is undefined
196. hether wrapA11 or wrapWater can be enabled In general internal coordinate wrapping by NAMD does not affect the calculation of colvars if each atom group satisfies one or more of the following i it is composed by only one atom ii it is used by a colvar component which does not make use of its center of geometry but only of pairwise distances distanceInv coordNum hBond alpha dihedralPC 129 iii it is used by a colvar component that ignores the ill defined Cartesian components of its center of mass such as the x and y components of a membrane s center of mass modeled with distanceZ iv it has all of its atoms within the same molecular fragment 10 3 4 Computational cost of colvars based on group size In parallel MD simulations the calculation of most interaction terms are spread over many compu tational nodes but the calculation of colvars is not parallelized Therefore additional calculations are executed by the node calculating the colvars and most importantly additional communication is added between the first node and the other nodes The latency tolerant design and dynamic load balancing of NAMD alleviate both factors however under some circumstances a noticeable performance impact may be observed To mitigate that atom groups should be kept relatively small up to a few thousands depending on the computational cost to simulate the system by itself 10 4 Collective variable components basis functions E
197. hich is prepended to the path returned by the pwd command To run on multiple machines you must add a pathfix option to your nodelist file For example group main pathfix tmp _mnt host alphai host alpha2 There are many other options to charmrun and for the nodelist file These are documented at in the Charm Installation and Usage Manual available at http charm cs uiuc edu manuals and a list of available charmrun options is available by running charmrun without arguments If your workstation cluster is controlled by a queueing system you will need build a nodelist file in your job script For example if your queueing system provides a HOST_FILE environment variable set NODES cat HOST_FILE set NODELIST TMPDIR namd2 nodelist echo group main gt NODELIST foreach node nodes echo host node gt gt NODELIST end NUMPROCS 2 NODES charmrun namd2 p NUMPROCS nodelist NODELIST lt configfile gt Note that NUMPROCS is twice the number of nodes in this example This is the case for dual processor machines For single processor machines you would not multiply 4NODES by two Note that these example scripts and the setenv command are for the csh or tcsh shells They must be translated to work with sh or bash 17 5 Shared Memory and Network Based Parallelism SMP Builds The Linux x86_64 ibverbs smp and Solaris x86_64 smp released binaries are based on smp builds of Charm that can be used
198. hin the chosen boundary conditions cartesian vector of atomic Cartesian coordinates The cartesian block defines a component returning a flat vector containing the Cartesian coordinates of all participating atoms in the order 11 Y1 21 En Yn 2n This component accepts the following keyword e atoms lt Group of atoms gt Context cartesian Acceptable Values Block atoms Description Defines the atoms whose coordinates make up the value of the component If rotateReference or centerReference are defined coordinates are evaluated within the moving frame of reference angle angle between three groups The angle block defines an angle and contains the three blocks group1 group2 and group3 defining the three groups It returns an angle in degrees within the interval 0 180 dihedral torsional angle between four groups The dihedral block defines a tor sional angle and contains the blocks group1 group2 group3 and group4 defining the four groups It returns an angle in degrees within the interval 180 180 The colvar module calculates all the distances between two angles taking into account periodicity For instance reference values for restraints or range boundaries can be defined by using any real number of choice e oneSiteSystemForce lt Measure system force on group 1 only gt Context angle dihedral Acceptable Values boolean Default Value no Description If this is set to yes
199. hod 5 2 Non bonded interactions NAMD has a number of options that control the way that non bonded interactions are calculated These options are interrelated and can be quite confusing so this section attempts to explain the behavior of the non bonded interactions and how to use these parameters 5 2 1 Van der Waals interactions The simplest non bonded interaction is the van der Waals interaction In NAMD van der Waals interactions are always truncated at the cutoff distance specified by cutoff The main option that effects van der Waals interactions is the switching parameter With this option set to on a smooth switching function will be used to truncate the van der Waals potential energy smoothly at the cutoff distance A graph of the van der Waals potential with this switching function is shown in Figure 1 If switching is set to off the van der Waals energy is just abruptly truncated at the cutoff distance so that energy may not be conserved 47 switchdist cutoff AER AR A A H A RRA SAA energy distance Figure 1 Graph of van der Waals potential with and without the application of the switching function With the switching function active the potential is smoothly reduced to 0 at the cutoff distance Without the switching function there is a discontinuity where the potential is truncated The switching function used is based on the X PLOR switching function The parameter switchdist specifies the dista
200. ical system Section 10 3 documents how to select atoms and section 10 4 lists all of the available functional forms which we call colvar components Finally section 10 5 lists the available methods and algorithms to perform biased simulations and multidimensional analysis of colvars 10 1 3 Input state file optional Aside from the colvars configuration an optional input state file may be provided to load the relevant data from a previous simulation The name of this file is provided as a value to the keyword colvarsInput 10 1 4 Output files During a simulation with collective variables defined the following three output files are written e a state file named outputName colvars state this file is in ASCII format regardless of the value of binaryOutput in the NAMD configuration to continue the simulation the name of this file must be included in the configuration of the next run using colvarsInput together with the other NAMD output files e if the NAMD parameter restartFreq or the parameter colvarsRestartFrequency is larger than zero a restart file named restartName colvars state is written every that many steps this file is equivalent to the final state file e if the parameter colvarsTrajFrequency is greater than 0 default 100 a trajectory file is written during the simulation its name is outputName colvars traj unlike the state file it is not needed to restart a simulation but can be used later for post proce
201. icalBCr1 parameter 75 cylindricalBCr2 parameter 75 dcdF ile command 20 DCDfile parameter 17 25 DCDfreq parameter 26 DCDUnitCell parameter 26 delatom psfgen command 42 dielectric parameter 50 differenceVector colvars eigenvector key word 138 drude parameter 60 drudeBondConst parameter 60 drudeBondLen parameter 60 drudeDamping parameter 60 drudeNbTholeCut parameter 60 drudeTemp parameter 60 dummyAtom colvars atom group keyword 127 dumpPartialFreeEnergyFile metadynamics keyword 156 colvars eField parameter 17 92 eFieldFreq parameter 17 eFieldNormalized parameter 93 eFieldOn parameter 92 eFieldPhase parameter 17 enableFitGradients colvars atom group key word 129 enableForces colvars atom group keyword 129 error message Atoms moving too fast 89 Bad global exclusion count 89 exclude parameter 50 ExcludeFromPressure parameter 87 ExcludeFromPressureCol parameter 87 ExcludeFromPressureFile parameter 87 exit command 18 expandBoundaries colvars colvar keyword 120 expDenom colvars coordNum keyword 135 expNumer colvars coordNum keyword 135 exponent colvars distanceInv keyword 133 extCoordFilename parameter 112 extended Fluctuation colvars colvar keyword 122 extendedLagrangian colvars colvar keyword 122 extendedLangevinDamping colvars keyword 123 extendedSystem parameter 72 extended Temp colvars colvar keyword 122 extended TimeConstant colvars colvar
202. id3 p aid4 The force to be applied on each atom is proportional to its corresponding gradient addforce aid1 vecscale g1 force addforce aid2 vecscale g2 force addforce aid3 vecscale g3 force addforce aid4 vecscale g4 force 108 9 11 Tcl Boundary Forces While the tclForces interface described above is very flexible it is only efficient for applying forces to a small number of pre selected atoms Applying forces individually to a potentially large number of atoms such as applying boundary conditions is much more efficient with the tc1BC facility described below e tclBC lt are Tcl boundary forces active gt Acceptable Values on or off Default Value off Description Specifies whether or not Tcl interface is active If it is set to off then no Tcl code is executed If it is set to on then Tcl code specified in the tc1BCScript parameter is executed e tclBCScript lt input for Tcl interface gt Acceptable Values script Description Must contain the script itself between and may include multiple lines This parameter may occur only once The script s should perform any required initialization on the Tcl interpreter and define a procedure calcforces lt step gt lt unique gt args to be called every timestep e tclBCArgs lt extra args for tclBC calcforces command gt Acceptable Values args Description The string or Tcl list provided by this option is appended to the tc
203. ied However the torque applied to the atom can be calculated as a vector product torque F x normal Finally the torque applied to the atom with respect to the axis is the projection of the torque on the axis i e torquepro torque v If there are atoms that have to be constrained but not moved this implementation is not suitable because it will move all reference positions Only one of the moving and rotating constraints can be used at a time Using very soft springs for rotating constraints leads to the system lagging behind the reference positions and then the force is applied along a direction different from the ideal direction along the circular path Pulling on N atoms at the same time with a spring of stiffness K amounts to pulling on the whole system by a spring of stiffness NK so the overall behavior of the system is as if you are pulling with a very stiff spring if N is large In both moving and rotating constraints the force constant that you specify in the constraints pdb file is multiplied by 2 for the force calculation i e if you specified K 0 5 keal mol A in the pdb file the force actually calculated is F 2K R X 1 keal mol A7 R X SMD feature of namd2 does the calculation without multiplication of the force constant specified in the config file by 2 e rotConstraints lt Are rotating constraints active gt Acceptable Values on or off Default Value off Description Should rotating restraints be
204. ifies whether or not harmonic constraints are active If it is set to off then no harmonic constraints are computed If it is set to on then harmonic constraints are calculated using the values specified by the parameters consref conskfile conskcol and consexp e consexp lt exponent for harmonic constraint energy function gt Acceptable Values positive even integer Default Value 2 Description Exponent to be use in the harmonic constraint energy function This value must be a positive integer and only even values really make sense This parameter is used only if constraints is set to on e consref lt PDB file containing constraint reference positions gt Acceptable Values UNIX file name Description PDB file to use for reference positions for harmonic constraints Each atom that has an active constraint will be constrained about the position specified in this file e conskfile lt PDB file containing force constant values gt Acceptable Values UNIX filename Description PDB file to use for force constants for harmonic constraints e conskcol lt column of PDB file containing force constant gt Acceptable Values X Y Z 0 or B Description Column of the PDB file to use for the harmonic constraint force constant This parameter may specify any of the floating point fields of the PDB file either X Y Z occupancy or beta coupling temperature coupling Regardless of which column is used a value of 0 indicates that the at
205. ileEwaldX 16 pressureProfileEwaldY 16 pressureProfileEwaldZ 16 set ts 0 firstTimestep ts coorfile open dcd pp03 dcd while coorfile read 1 incr ts 500 firstTimestep ts run 0 194 coorfile close 195 15 Translation between NAMD and X PLOR configuration pa rameters NAMD was designed to provide many of the same molecular dynamics functions that X PLOR provides As such there are many similarities between the types of parameters that must be passed to both X PLOR and NAMD This section describes relations between similar NAMD and X PLOR parameters e NAMD Parameter cutoff X PLOR Parameter CTOFNB When full electrostatics are not in use within NAMD these parameters have exactly the same meaning the distance at which electrostatic and van der Waals forces are truncated When full electrostatics are in use within NAMD the meaning is still very similar The van der Waals force is still truncated at the specified distance and the electrostatic force is still computed at every timestep for interactions within the specified distance However the NAMD integration uses multiple time stepping to compute electrostatic force interactions beyond this distance every stepspercycle timesteps e NAMD Parameter vdwswitchdist X PLOR Parameter CTONNB Distance at which the van der Waals switching function becomes active e NAMD Parameter pairlistdist X PLOR Parameter CUTNb Distance within which interaction pairs will be
206. imulation run this is a change from NAMD 2 5 when nonbonded contri butions to the Ewald sum were always computed offline If the simulations are performed using PME the Ewald contribution should be estimated using a separate offline calculation based on the saved trajectory files The nonbonded contribution using a cutoff different from the one used in the simulation may also be computed offline in the same fashion as for Ewald if desired Pressure profile calculations may be performed in either constant volume or constant pressure conditions If constant pressure is enabled the slabs thickness will be rescaled along with the unit cell the dcdUnitCell option will also be switched on so that unit cell information is stored in the trajectory file NAMD 2 6 now reports the lateral pressure partitioned by interaction type Three groups are reported kinetic rigid bond restraints referred to as internal bonded and nonbonded If Ewald pressure profile calculations are active the Ewald contribution is reported in the nonbonded section and no other contributions are reported NAMD 2 6 also permits the pressure profile to be partitioned by atom type Up to 15 atom groups may be assigned and individual contribution of each group for the internal pressures and the pairwise contributions of interactions within and between groups for the nonbonded and bonded pressures are reported in the output file e pressureProfile lt compute pre
207. in the Ca Ca Ca angle gt Context alpha Acceptable Values positive decimal Default Value 15 Description This option sets the angle tolerance used in the score function 46 e hBondCutoff lt Hydrogen bond cutoff gt Context alpha Acceptable Values positive decimal Default Value 3 3 A Description Equivalent to the cutoff option in the hBond component e hBondExpNumer lt Hydrogen bond numerator exponent gt Context alpha Acceptable Values positive integer Default Value 6 Description Equivalent to the expNumer option in the hBond component e hBondExpDenom lt Hydrogen bond denominator exponent gt Context alpha Acceptable Values positive integer Default Value 8 Description Equivalent to the expDenom option in the hBond component This component returns positive values always comprised between 0 lowest a helical score and 1 highest a helical score 142 dihedralPC protein dihedral pricipal component The block dihedralPC defines the parameters to calculate the projection of backbone dihedral angles within a protein seg ment onto a dihedral principal component following the formalism of dihedral principal com ponent analysis dPCA proposed by Mu et al 53 and documented in detail by Altis et al 2 Given a peptide or protein segment of N residues each with Ramachandran an gles and 4 dPCA rests on a variance covariance analysis of the 4 N 1 variables cos w1 sin w1 cos 2
208. ine in the configuration files consists of a keyword identifying the option being specified and a value which is a parameter to be used for this option The keyword and value can be separated by only white space 15 keyword value or the keyword and value can be separated by an equal sign and white space keyword value Blank lines in the configuration file are ignored Comments are prefaced by a and may appear on the end of a line with actual values keyword value This is a comment or may be at the beginning of a line This entire line is a comment Some keywords require several lines of data These are generally implemented to either allow the data to be read from a file keyword filename or to be included inline using Tcl style braces keyword lots of data The specification of the keywords is case insensitive so that any combination of upper and lower case letters will have the same meaning Hence DCDfile and dcdfile are equivalent The capitalization in the values however may be important Some values indicate file names in which capitalization is critical Other values such as on or off are case insensitive 2 2 2 Tcl scripting interface and features When compiled with Tcl all released binaries the config file is parsed by Tcl in a fully backwards compatible manner with the added bonus that any Tcl command may also be used This alone allows e the source command to include other files works w o Tc
209. ing and Efficient Simulation Method for Biomolecules D Hamelberg J Mongan and J A McCammon J Chem Phys 120 11919 11929 2004 e Implementation of Accelerated Molecular Dynamics in NAMD Y Wang C Harrison K Schulten and J A McCammon Comp Sci Discov 4 015002 2011 12 1 1 Theoretical background In the original form of aMD 30 when the system s potential energy falls below a threshold energy E a boost potential is added such that the modified potential V r is related to the original potential V r via V r V r AV r 63 where AV r is the boost potential AV r 0 V r gt E 64 2 wae V r lt E As shown in the following figure the threshold energy E controls the portion of the potential surface affected by the boost while the acceleration factor determines the shape of the modified potential Note that cannot be set to zero otherwise the derivative of the modified potential is discontinuous From an aMD simulation the ensemble average 4 of an observable A r can be calculated using the following reweighting procedure A r exp BAV 1 exp BAV 1 in which G 1 kgT and and represent the ensemble average in the original and the aMD ensembles respectively Currently aMD can be applied in three modes in NAMD aMDd aMDT and aMDdual 74 The boost energy is applied to the dihedral potential in the aMDd mode the default mode and to the total
210. interpretations along the lines of the free energy for switching on the van der Waals context of the simulation setup and parameters used in this case and is not informative in a broader interactions for the atoms of partition 1 was 6 35kcal mol This is only correct in the very narrow The choice of values will depend on the application but in general it is important to examine the shape of the curve to ensure that sampling is adequate to give a good estimate of the integral In system see Figure 10 particular it will be necessary to sample more finely towards the end points in order to accurately account for the strong repulsive van der Waals forces encountered when inserting particles into a 174 12 Accelerated Sampling Methods 12 1 Accelerated Molecular Dynamics Accelerated molecular dynamics aMD 30 is an enhanced sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system The method modifies the potential energy landscape by raising energy wells that are below a certain threshold level while leaving those above this level unaffected As a result barriers separating adjacent energy basins are reduced allowing the system to sample conformational space that cannot be easily accessed in a classical MD simulation Please include the following two references in your work using the NAMD implementation of aMD e Accelerated Molecular Dynamics A Promis
211. ints along the axis and a periodic cell size which just contains the grid The Unshifted case shows how the pontential is not smooth when mgridforcevoff is not specified or set to zero The Shifted potential shows the grid that results when mgridfocevoff is set so that the wrapped potential is offset so that the potential has constant slope at the periodic boundaries A velocity vector Y movingConsVel needs to be specified The way the moving constraints work is that the moving reference position is calculated ev ery integration time step using Eq 30 where is in A timestep and t is the current timestep i e firstTimestep plus however many timesteps have passed since the beginning of NAMD run Therefore one should be careful when restarting simulations to appropriately update the firstTimestep parameter in the NAMD configuration file or the reference position specified in the reference PDB file NOTE NAMD actually calculates the constraints potential with U k x zo and the force with F dk x xo where d is the exponent consexp The result is that if one specifies some value for the force constant k in the PDB file effectively the force constant is 2k in calculations This caveat was removed in SMD feature The following parameters describe the parameters for the moving harmonic constraint feature of NAMD e movingConstraints lt Are moving constraints active gt Acceptable Values on or off Default Value off Descript
212. ion Should moving restraints be applied to the system If set to on then movingConsVel must be defined May not be used with rotConstraints 97 e movingConsVel lt Velocity of the reference position movement gt Acceptable Values vector in timestep Description The velocity of the reference position movement Gives both absolute value and direction 9 5 Rotating Constraints The constraints parameters are specified in the same manner as for usual static harmonic con straints The reference positions of all constrained atoms are then rotated with a given angular velocity about a given axis If the force constant of the constraints is sufficiently large the con strained atoms will follow their reference positions A rotation matrix M about the axis unit vector v is calculated every timestep for the angle of rotation corresponding to the current timestep angle Qt where Q is the angular velocity of rotation From now on all quantities are 3D vectors except the matrix M and the force constant K The current reference position R is calculated from the initial reference position Ry at t 0 R M Ro P P where P is the pivot point Coordinates of point N can be found as N P R P v v Normal from the atom pos to the axis is similarly normal P X P v v X The force is as usual F K R X This is the force applied to the atom in NAMD see below NAMD does not know anything about the torque appl
213. ion of the Random Acceleration Molecular Dynamics RAMD simulation method in NAMD The RAMD method can be used to carry out molecular dynamics MD simulations with an additional randomly oriented acceleration applied to the center of mass of one group of atoms referred below as ligand in the system It can for example be used to identify egress routes for a ligand from a buried protein binding site Since its original implementation in the ARGOS ref 1 2 program the method has been also implemented in AMBER 8 ref 3 and CHARMM ref 4 The first implementation of 183 RAMD in NAMD using a tcl script available as supplementary material in ref 6 provided only limited functionality compared to the AMBER 8 implementation In the current implementation the RAMD method can be performed in 2 flavors i pure RAMD simulations in which the randomly oriented acceleration is applied continuously and ii combined RAMD MD simulations in which RAMD steps alternate with standard MD steps Additional information is found in the README file in the lib ramd directory The user is encouraged to carefully read this information before starting production runs The three required scripts are stored in lib ramd scripts i ramd 4 0 tcl defines the sim ulation parameters and passes them from the NAMD configuration file to the main script ii ramd 4 0_script tcl adds the randomly oriented force and performs all related
214. ions except for the value of this option e replicasRegistry lt Multiple replicas database file gt Context metadynamics Acceptable Values UNIX filename Default Value name replica files txt Description If multipleReplicas is on this option sets the path to the replicas database file e replicaUpdateFrequency lt How often hills are communicated between replicas gt Context metadynamics Acceptable Values positive integer Default Value newHillFrequency Description If multipleReplicas is on this option sets the number of steps after which each replica re reads the other replicas files The lowest meaningful value of this number is newHillFrequency If access to the file system is significantly affecting the simulation performance this number can be increased at the price of reduced synchronization between replicas Values higher than colvarsRestartFrequency may not improve performance sig nificantly e dumpPartialFreeEnergyFile lt Periodically write the contribution to the PMF from this replica gt Context metadynamics Acceptable Values boolean Default Value on Description When multipleReplicas is on tje file outputName pmf contains the combined PMF from all replicas Enabling this option produces an additional file output Name partial pmf which can be useful to quickly monitor the contribution of each replica to the PMF The requirements for this option are the same as dumpFreeEnergyFile Compatibility
215. ique group and monomer identifiers in increasing order e symmetryMatrixFile lt File for transformation matrices gt Acceptable Values Path to matrix file Description The symmetryMatrixFile is a path to a file that contains a list of trans formation matrices to make the monomers overlap The file should contain one and only one matrix for each monomer in the order of monomer ID designated in the symmetryFile Each symmetry group should have its own symmetryMatrixFile file containing only the ma trices used by the monomers in that group These should be formatted with spaces between columns and NO spaces between rows as follows 1000 0100 0010 0001 with different matrices separated by a single blank line and no line before the first or after the last matrix This file is OPTIONAL Leave this line out to have namd generate the transformations for you e symmetryFirstStep lt first symmetry restraint timestep gt Acceptable Values Non negative integer Default Value 0 Description 100 e symmetryLastStep lt last symmetry restraint timestep gt Acceptable Values Positive integer Default Value infinity Description Symmetry restraints are applied only between symmetryFirstStep and symmetryLastStep Use these settings with caution and ensure restraints are only being applied when necessary e g not during equilibration 9 7 Targeted Molecular Dynamics TMD In TMD subset of atoms in the simulation is guided toward
216. ires e the program psfgen from any NAMD distribution e the CHARMM topology and parameter files top_al122_prot inp and par_a1122_prot inp from http www pharmacy umaryland edu faculty amackere force fields htm and e the BPTI PDB file 6PTI pdb available from the Protein Data Bank at http www pdb org by searching for 6PTI and downloading the complete structure file in PDB format Building the BPTI structure In this demo we create the files bpti psf and bpti pdb in the output directory which can then be used for a simple NAMD simulation File bpti_example tcl Requirements topology file top_al122_prot inp in directory toppar PDB file 6PTI pdb in current directory Create working directory remove old output files mkdir p output rm f output 6PTI_protein pdb output 6PTI_water pdb 1 Split input PDB file into segments grep v HETATM 6PTI pdb gt output 6PTI_protein pdb grep HOH 6PTI pdb gt output 6PTI_water pdb 2 Embed the psfgen commands in this script psfgen lt lt ENDMOL 3 Read topology file topology toppar top_al122_prot inp 4 Build protein segment segment BPTI 34 pdb output 6PTI_protein pdb 5 Patch protein segment patch DISU BPTI 5 BPTI 55 patch DISU BPTI 14 BPTI 38 patch DISU BPTI 30 BPTI 51 6 Read protein coordinates from PDB file pdbalias atom ILE CD1 CD formerly alias atom coordpdb output 6PTI_protein pdb BPTI 7 Build water segment
217. is really being modified is the value of a coupling parameter ALJ or elec that scales the interactions e if set to 0 the latter are off if set to 1 they are on in lieu of the actual value of A provided by the user Rin 2 6 Rin 2 3 V io A ij ij ij e ec n 58 NB rij LJEij 6 1 ca 6 1 5 toa ane A It is also worth noting that the free energy calculation does not alter intermolecular bonded potentials e g bond stretch valence angle deformation and torsions in the course of the sim ulation In calculations targeted at the estimation of free energy differences between two states characterized by distinct environments e g a ligand bound to a protein in the first simulation and solvated in water in the second as is the case for most free energy calculations that make use of a thermodynamic cycle perturbation of intramolecular terms may by and large be safely avoided 10 This property is controlled by the alchDecouple keyword described in 11 1 2 Free Energy Perturbation Within the FEP framework 8 16 17 26 41 48 70 73 79 the free energy difference between two alternate states a and b is expressed by 166 AA In exp 8 Ho x Pr Hal Pa a 59 Here 87 kgT where kg is the Boltzmann constant T is the temperature Ha X Pr and Hi X Px are the Hamiltonians describing states a and b respectively denotes an ensemble average over configurations
218. ist parameter is also used to determine the minimum patch size Unless the splitPatch parameter is explicitly set to position hydrogen atoms will be placed on the same patch as the mother atom to which they are bonded These hydrogen groups are then distance tested against each other using only a cutoff increased by the the value of the hgroupCutoff parameter The size of the patches is also increased by this amount NAMD functions correctly even if a hydrogen atom and its mother atom are separated by more than half of hgroupCutoff by breaking that group into its individual atoms for distance testing Margin violation warning messages are printed if an atom moves outside of a safe zone surrounding the patch to which it is assigned indicating that pairlistdist should be increased in order for forces to be calculated correctly and energy to be conserved Margin violations mean that atoms that are in non neighboring patches may be closer than the cutoff distance apart This may sometimes happen in constant pressure simulations when the cell shrinks since the patch grid remains the same size The workaround is to increase the margin parameter so that the simulation starts with fewer larger patches Restarting the simulation will 88 pairlist distance cutoff gt 0 lt Figure 4 Depiction of the difference between the cutoff distance and the pair list distance The pair list distance specifies a sphere that is slightly larger than that of t
219. istance Acceptable Values boolean Default Value no Description By default in calculations with periodic boundary conditions the distance component returns the distance according to the minimum image convention If this parame ter is set to yes PBC will be ignored and the distance between the coordinates as maintained internally will be used This is only useful in a limited number of special cases e g to de scribe the distance between remote points of a single macromolecule which cannot be split across periodic cell boundaries and for which the minimum image distance might give the wrong result because of a relatively small periodic cell 131 oneSiteSystemForce lt Measure system force on group 1 only gt Context distance Acceptable Values boolean Default Value no Description If this is set to yes the system force is measured along a vector field see equation 53 in section 10 5 1 that only involves atoms of group1 This option is only useful for ABF or custom biases that compute system forces See section 10 5 1 for details The value returned is a positive number in A ranging from 0 to the largest possible interatomic distance within the chosen boundary conditions with PBCs the minimum image convention is used unless the forceNoPBC option is set distanceZ projection of a distance vector on an axis The distanceZ block defines a distance projection component which can be seen as measuring the distanc
220. ith the indexGroup keyword Other supported methods to select atoms are described in 10 3 e analysis lt Turn on run time statistical analysis gt Context global Acceptable Values boolean Default Value off Description If this flag is enabled each colvar is instructed to perform whatever run time statistical analysis it is configured to such as correlation functions or running averages and standard deviations See section 10 2 5 for details The example below defines the same configuration shown in Fig 6 The options within the colvar blocks are described in 10 2 and 10 4 the ones within the harmonic and histogram blocks 116 in 10 5 Note except colvar none of the keywords shown is mandatory colvar difference of two distances name d width 0 2 0 2 A of estimated fluctuation width distance componentCoeff 1 0 group1 atomNumbers 1 2 group2 atomNumbers 3 4 5 distance componentCoeff 1 0 group1 atomNumbers 7 group2 atomNumbers 8 9 10 J y colvar name c coordNum cutoff 6 0 group1 atomNumbersRange 1 10 group2 atomNumbersRange 11 20 colvar name alpha alpha psfSegID PROT residueRange 1 10 J y harmonic colvars dc centers 3 0 4 0 forceConstant 5 0 histogram colvars c alpha 117 Section 10 2 explains how to define a colvar and its behavior regardless of its specific functional form To define colvars that are appropriate to a specific phys
221. itial_pdb_file the initial coordinate pdb file for show_replicas vmd 182 e fit_pdb file the coodinates that frames are fit to by show_replicas vmd e g a folded structure The lib replica example directory contains all files needed to fold a 66 atom model of a deca alanine helix e alanin base namd basic config options for NAMD e alanin params parameters e alanin psf structure e unfolded pdb initial coordinates e alanin pdb folded structure for fitting in show_replicas vmd e fold alanin conf config file for replica_exchange tcl script e job0 conf config file to start alanin folding for 10 ns e job1 conf config file to continue alanin folding another 10 ns and e load_all vmd load all output into VMD and color by replica index The fold_alanin conf config file contains the following settings set num_replicas 8 set min_temp 300 set max_temp 600 set steps_per_run 1000 set num_runs 10000 num_runs should be divisible by runs_per_frame frames_per_restart set runs_per_frame 10 set frames_per_restart 10 set namd_config_ file alanin_base namd set output_root output s fold_alanin directories must exist the following used only by show_replicas vmd set psf_file alanin psf set initial_pdb_file unfolded pdb set fit_pdb_file alanin pdb 12 5 Random acceleration molecular dynamics simulations The lib ramd directory stores the tcl scripts and the example files for the implementat
222. l only be performed when the current step is equal to or higher than accelMDFirstStep and equal to or lower than accelMDLastStep Otherwise regular MD will be performed Note that the accelMDLastStep parameter only has an effect when it is positive When accelMDLastStep is set to zero the default aMD is open ended and will be performed till the end of the simulation accelMDOutFreq lt Frequency in steps of aMD output gt Acceptable Values Positive integer Default Value 1 Description An aMD output line will be printed to the log file at the frequency specified by accelMDOutFreq The aMD output will contain the boost potential dV at the current timestep the average boost potential 1W AVG since the last aMD output and various potential energy values at the current timestep The boost potential dV can be used to reconstruct the ensemble average described earlier 12 2 Adaptive Tempering Adaptive tempering is akin to a single copy replica exchange method for dynamically updating the simulation temperature The temperature T is a new random variable in the range T min Tmax that is governed by the equation dE dT E E T 1 T sqrt 2 T where is Gaussian white noise The effect is that when the potential energy for a given structure is lower than the so far calculated average energy the temperature is lowered Conversely when the current energy is higher than the average energy the temperature is raised The eff
223. l spacing for a desired grid spacing h is guaranteed to be within the interval Eh Sh MSMQuality lt select the approximation quality gt Acceptable Values 0 1 2 3 4 Default Value 0 Description This parameter offers a simplified way to select higher order interpolation and splitting for MSM The available choices are 0 sets C cubic p 3 interpolation with C Taylor splitting 1 sets C1 Hermite p 4 interpolation with C Taylor splitting 2 sets C quintic p 5 interpolation with C Taylor splitting 3 sets C septic p 7 interpolation with C Taylor splitting 4 sets C nonic p 9 interpolation with C Taylor splitting We presently recommend using the default selection which has been validated to correctly reproduce the PME results 92 and discourage use of the higher order interpolation schemes as they are still under development With cubic interpolation MSM now gets roughly half the performance of PME Comparable performance and better scaling for MSM have been observed with the optimizations described in Ref 32 which will be available shortly There is generally a tradeoff between quality and performance Empirical results show that the C interpolation schemes offer a little better accuracy than the alternative interpolation schemes that have greater continuity Also better accuracy has been observed by using a splitting function with C 1 21 continuity where p is the order
224. l too e the print command to display messages puts to stdout fails on some platforms e environment variables through the env array Senv USER and e user defined variables set base sim23 dcdfile base dcd Additional features include e The callback command takes a 2 parameter Tcl procedure which is then called with a list of labels and a list of values during every timestep allowing analysis formatting whatever e The run command takes a number of steps to run overriding the now optional numsteps parameter which defaults to 0 and can be called repeatedly You can run 0 just to get energies Normally the preceeding timestep is repeated to account for any modifications to the energy function this can be avoided with run norepeat 16 The minimize command is similar to run and performs minimization for the specified number of force evaluations The startup command will trigger simulation startup as would the first run or minimize command but without any force energy evaluation Configuration file parameter introspection is supported by invoking a case insensitive pa rameter keyword with no argument e g numsteps and by the helper commands isset and istrue Note that keywords are not parsed until the first run command and before this values are treated as unformatted strings so for example eFieldOn and
225. lBC calcforces command arguments This parameter may appear multiple times during a run in order to alter the parameters of the boundary potential function The script provided in tclBCScript and the calcforces procedure it defines are executed in multiple Tcl interpreters one for every processor that owns patches These tcl1BC interpreters do not share state with the Tcl interpreter used for tclForces or config file parsing The calcforces procedure is passed as arguments the current timestep a unique flag which is non zero for exactly one Tcl interpreter in the simulation that on the processor of patch zero and any arguments provided to the most recent tclBCArgs option The unique flag is useful to limit printing of messages since the command is invoked on multiple processors The print vecadd vecsub vecscale getbond getangle getdihedral anglegrad and dihedralgrad commands described under tclForces are available at all times The wrapmode lt mode gt command available in the tclBCScript or the calcforces procedure determines how coordinates obtained in the calcforces procedure are wrapped around periodic boundaries The options are e patch default the position in NAMD s internal patch data structure requires no extra calculation and is almost the same as cell e input the position corresponding to the input files of the simulation e cell the equivalent position in the unit cell centered on the cell0Origin 1
226. lating the linear potential 161 e updateFrequency lt The duration of updates gt Context alb Acceptable Values An integer Description This is N the number of simulation steps to use for each update to the bias This determines how long the system requires to equilibrate after a change in force constant N 2 how long statistics are collected for an iteration N 2 and how quickly energy is added to the system at most A 2N where A is the forceRange Until the force constant has converged the method as described is an optimization procedure and not an integration of a particular statistical ensemble It is important that each step should be uncorrelated from the last so that iterations are independent Therefore N should be at least twice the autocorrelation time of the collective variable The system should also be able to dissipate energy as fast as N 2 which can be done by adjusting thermostat parameters Practically N has been tested successfully at significantly shorter than the autocorrelation time of the collective variables being biased and still converge correctly e forceRange lt The expected range of the force constant in units of energy gt Context alb Acceptable Values A space separated list of decimal numbers Default Value 3 kT Description This is largest magnitude of the force constant which one expects If this parameter is too low the simulation will not converge If it is too high the simulation will waste
227. lation in order to exclude startup costs and allow for initial load balancing Multicore builds scale well within a single node On machines with more than 32 cores it may be necessary to add a communication thread and run on one fewer core than the machine has On a 48 core machine this would be run as namd2 p47 commthread Performance may also benefit from setting CPU affinity using the setcpuaffinity pemap jmapj commap jmapj options described in CPU Affinity above Experimentation is needed We provide standard UDP TCP and ibverbs InfiniBand precompiled binaries for Linux clusters The TCP version may be faster on some networks but the UDP version now performs well on gigabit ethernet The ibverbs version should be used on any cluster with InfiniBand and for any other high speed network you should compile an MPI version SMP builds generally do not scale as well across nodes as single threaded non SMP builds because the communication thread is both a bottleneck and occupies a core that could otherwise be used for computation As such they should only be used to reduce memory consumption or if for scaling reasons you are not using all of the cores on a node anyway and you should run benchmarks to determine the optimal configuration Extremely short cycle lengths less than 10 steps will limit parallel scaling since the atom migration at the end of each cycle sends many more messages than a normal force evaluation Increasing margin
228. ld continue etc Section 2 2 1 describes how options are specified within a NAMD configuration file Section 2 2 4 lists the parameters which are required to run a basic simulation Section 15 describes the relation between specific NAMD and X PLOR dynamics options Several sample NAMD configuration files are shown in section 16 During execution NAMD will change to the directory containing the configuration file so that all file paths in the configuration file are relative to the configuration file directory Multiple configuration files may be specified on the command line and the will be read in order but all file paths will be relative to the first configuration file to call a run or minimize or startup command or to the last configuration file if run is not called Commands or parameters may also be specified directly on the command line via keyword value argument pairs for example outputenergies 100 run 100 checkpoint This may be used to include multiple configuration files without altering the working directory via source path to second conf Note that escaping or quoting of com mand line parameter values containing spaces may be difficult or impossible on some systems due to multiple levels of scripts called during the NAMD parallel launch process and because the keyword and value are simply merged into a single string that is passed to the Tcl interpreter 2 2 1 Configuration parameter syntax Each l
229. ld contribution to the pressure profile will be computed For trajectory analysis the recommended way to use this option is to use the NAMD Tel scripting interface as described in Sec 2 2 2 to run for 0 steps so that NAMD prints the pressure profile without performing any dynamics The Ewald sum method is as described in Sonne et al JCP 122 2005 The number of k vectors to use along each periodic cell dimension is specified by the pressureProfileEwaldn parameters described below pressureProfileEwaldX lt Ewald grid size along X gt Acceptable Values Positive integer Default Value 10 Description pressureProfileEwaldY lt Ewald grid size along Y gt Acceptable Values Positive integer Default Value 10 Description pressureProfileEwaldZ lt Ewald grid size along Z gt Acceptable Values Positive integer Default Value 10 Description pressureProfileAtomTypes lt Number of atom type partitions gt Acceptable Values Positive integer Default Value 1 Description If pressureProfileAtomTypes is greater than 1 NAMD will calculate the separate contributions of each type of atom to the internal bonded nonbonded and total pressure In the case of the internal contribution there will be n pressure profile data sets reported on each PPROFILEINTERNAL line where n is the number of atom types All the partial pressures for atom type 1 will be followed by those for atom type 2 and so forth The other three pressure profi
230. le reports will contain n n 1 2 data sets For example if there are n 3 atom types the six data sets arising from the three inter partition and the three intra partition interactions will be reported in the following order 1 1 1 2 1 8 2 2 2 3 3 3 The total pressure profile reported on the PRESSUREPROFILE line will contain the internal contributions in the data sets corresponding to 1 1 2 2 etc 193 e pressureProfileAtomTypesFile lt Atom type partition assignments gt Acceptable Values PDB file Default Value coordinate file Description If pressureProfileAtomTypes is greater than 1 NAMD will assign atoms to types based on the corresponding value in pressureProfileAtomTypesCol The type for each atom must be strictly less than pressureProfileAtomTypes e pressureProfileAtomTypesCol lt pressureProfileAtomTypesFile PDB column gt Acceptable Values PDB file Default Value B Description Here is an example snippet from a NAMD input that can be used to compute the Ewald component of the pressure profile It assumes that the coordinates were saved in the dcd file pp03 dcd every 500 timesteps Pme on PmeGridSizeX 64 PmeGridSizeY 64 PmeGridSizeZ 64 exclude scaled1 4 1 4scaling 1 0 switching on switchdist 9 cutoff 10 pairlistdist 11 pressureProfile on pressureProfileSlabs 30 pressureProfileFreq 100 pressureProfileAtomTypes 6 pressureProfileAtomTypesFile atomtypes pdb pressureProfileEwald on pressureProf
231. lgorithm is assumed to have converged when all constrained bonds differ from the nominal bond length by less than this amount e rigidIterations lt maximum ShakeH iterations gt Acceptable Values positive integer Default Value 100 Description The maximum number of iterations ShakeH will perform before giving up on constraining the bond lengths If the bond lengths do not converge a warning message is printed and the atoms are left at the final value achieved by ShakeH Although the default value is 100 convergence is usually reached after fewer than 10 iterations 61 e rigidDieOnError lt maximum ShakeH iterations gt Acceptable Values on or off Default Value on Description Exit and report an error if rigid Tolerance is not achieved after rigidItera tions e useSettle lt Use SETTLE for waters gt Acceptable Values on or off Default Value on Description If rigidBonds are enabled then use the non iterative SETTLE algorithm to keep waters rigid rather than the slower SHAKE algorithm 5 6 2 Harmonic restraint parameters The following describes the parameters for the harmonic restraints feature of NAMD For historical reasons the terminology of harmonic constraints has been carried over from X PLOR This feature allows a harmonic restraining force to be applied to any set of atoms in the simulation e constraints lt are constraints active gt Acceptable Values on or off Default Value off Description Spec
232. lices on each non continuous face of the grid and border grid values are computed so that the force felt by an atom outside the grid goes to zero If the grid is continuous along a particular dimension atoms outside the grid are affected by a potential that is interpolated from the grid and its corresponding periodic image along that dimension To calculate the force on an atom due to the grid the atom s coordinates are transformed according to the current basis vectors of the simulation box to a coordinate frame that is centered at the center of the specified grid Note that the size and spatial coordinates of the grid remain fixed and are not scaled as the size of the simulation box fluctuates For atoms within the grid the force is computed by analytically determining the gradient of the tricubic polynomial used to interpolate the potential from surrounding grid values For atoms outside the grid the state of the mgridforcecont 1 2 3 determine whether the force is zero or computed from the images of the grid as described above Note that if the grid is ever larger than the periodic box it is truncated at the edge of that box The consequence of this is that the computed potential will not vary smoothly at the edges introducing numerical instability NAMD also supports non uniform grids allowing regions of a grid to be defined at higher resolution Non uniform grids are structured hierarchically with a single maingrid which has one or more sub
233. ll the PMF files gt Context metadynamics Acceptable Values boolean Default Value off Description When writeFreeEnergyFile and this option are on the step number is included in the file name Activating this option can be useful to follow more closely the convergence of the simulation by comparing PMFs separated by short times Note when Gaussian hills are deposited near lowerBoundary or upperBoundary see 10 2 1 and interpolating grids are used default behavior their truncation can give rise to accumulating errors In these cases as a measure of fault tolerance all Gaussian hills near the boundaries are included in the output state file and are recalculated analytically whenever the colvar falls outside the grid s boundaries Such measure protects the accuracy of the calculation and can only be disabled by hardLowerBoundary or hardUpperBoundary To avoid gradual loss of performance and growth of the state file either one of the following solutions is recommended e enabling the option expandBoundaries so that the grid s boundaries are automatically recal culated whenever necessary the resulting pmf will have its abscissas expanded accordingly e setting lowerWal1 and upperWall well within the interval delimited by lowerBoundary and upperBoundary Performance tuning The following options control the computational cost of metadynamics calculations but do not affect results Default values are chosen to minimize such cost wi
234. lowing options define metadynamics calculations with more than one replica e multipleReplicas lt Multiple replicas metadynamics gt Context metadynamics Acceptable Values boolean Default Value off Description If this option is on multiple independent replica of the same system can be run at the same time and their hills will be combined to obtain a single PMF 59 Replicas are identified by the value of replicaID Communication is done by files each replica must be able to read the files created by the others whose paths are com municated through the file replicasRegistry This file and the files listed in it are 155 read every replicaUpdateFrequency steps Every time the colvars state file is written colvarsRestartFrequency the file outputName colvars name replicalD state is also written containing the state of the metadynamics bias for replicaID In the time steps between colvarsRestartFrequency new hills are temporarily written to the file outputName colvars name replicalD hills which serves as communication buffer These files are only required for communication and may be deleted after a new MD run is started with a different outputName e replicaID lt Set the identifier for this replica gt Context metadynamics Acceptable Values string Description If multipleReplicas is on this option sets a unique identifier for this replica All replicas should use identical collective variable configurat
235. lowing sections 10 1 1 NAMD parameters To enable a collective variables based calculation two parameters must be added to the NAMD configuration file colvars and colvarsConfig An optional third parameter colvarsInput can be used to continue a previous simulation The features described in this section were contributed by Giacomo Fiorin ICMS Temple University Philadel phia PA USA and J r me H nin IBPC CNRS Paris France Please send feedback and suggestions to the NAMD mailing list 113 biases colvars components distance d atoms 1 2 3 5 C 1 0 p 1 colvar d a z d i Me harmonic restraint distance d Ye K d d t w atoms 7 8 10 c c t w C 1 0 p 1 coord num coord atoms 1 10 11 20 radius 6 A colvar c coord histogram alpha c colvar alpha alpha alpha helix alpha residues 1 10 Figure 6 Graphical representation of a collective variables configuration The colvar called d is defined as the difference between two distances the first distance d1 is taken between the center of mass of atoms 1 and 2 and that of atoms 3 to 5 the second d2 between atom 7 and the center of mass of atoms 8 to 10 The difference d d d2 is obtained by multiplying the two by a coefficient C 1 or C 1 respectively The colvar called c is the coordi
236. ly sufficient as it is version and platform specific 5 2 5 MSM parameters The multilevel summation method MSM 32 is an alternative to PME for calculating full elec trostatic interactions The use of the FFT in PME has two drawbacks 1 it generally requires the use of periodic boundary conditions in which the simulation describes an infinite three dimensional lattice with each lattice cell containing a copy of the simulated system and 2 calculation of the FFT becomes a considerable performance bottleneck to the parallel scalability of MD simulations due to the many to many communication pattern employed MSM avoids the use of the FFT in its calculation instead employing the nested interpolation in real space of softened pair potentials which permits in addition to periodic boundary conditions the use of semi periodic boundaries in which there is periodicity along just one or two basis vectors or non periodic boundaries in which the simulation is performed in a vacuum Also better parallel scaling has been observed with MSM when scaling a sufficiently large system to a large number of processors See the MSM research web page http www ks uiuc edu Research msm for more information In order to use the MSM one need only specify MSM on in the configuration file For production use we presently recommend using the default MSMQuality 0 C1 cubic interpolation with C Taylor splitting which has been validated to correctl
237. ly the centers of the harmonic restraints during a simulations When the centers are changed continuously a steered MD in a collective variable space is carried out e targetCenters lt Steer the restraint centers towards these targets gt Context harmonic Acceptable Values space separated list of colvar values Description When defined the current centers will be moved towards these values during the simulation By default the centers are moved over a total of targetNumSteps steps by a linear interpolation in the spirit of Steered MD If targetNumStages is set to a nonzero value the change is performed in discrete stages lasting targetNumSteps steps each This second mode may be used to sample successive windows in the context of an Umbrella Sampling simulation When continuing a simulation run the centers specified in the configuration file lt colvarsConfig gt are overridden by those saved in the restart file lt colvarsInput gt To perform Steered MD in an arbitrary space of colvars it is sufficient to use this option and enable outputAppliedForce within each of the colvars involved e targetNumSteps lt Number of steps for steering gt Context harmonic Acceptable Values positive integer Description In single stage continuous transformations defines the number of MD steps required to move the restraint centers or force constant towards the values specified with targetCenters or targetForceConstant After the target values hav
238. ly when periodic boundary conditions PBCs are defined in the simulation and distanceZ s axis is parallel to a unit cell vector The following keywords can be used within periodic components and are illegal elsewhere e period lt Period of the component gt Context distanceZ Acceptable Values positive decimal Default Value 0 0 Description Setting this number enables the treatment of distanceZ as a periodic com ponent by default distanceZ is not considered periodic The keyword is supported but irrelevant within dihedral or spinAngle because their period is always 360 degrees 143 e wrapAround lt Center of the wrapping interval for periodic variables gt Context distanceZ dihedral or spinAngle Acceptable Values decimal Default Value 0 0 Description By default values of the periodic components are centered around zero ranging from P 2 to P 2 where P is the period Setting this number centers the interval around this value This can be useful for convenience of output or to set lowerWall and upperWall in an order that would not otherwise be allowed Internally all differences between two values of a periodic colvar follow the minimum image con vention they are calculated based on the two periodic images that are closest to each other Note linear or polynomial combinations of periodic components may become meaningless when components cross the periodic boundary Use such combinations carefully estimate the range o
239. mble The Langevin piston Nose Hoover method in NAMD is a combination of the Nose Hoover constant pressure method as described in GJ Martyna DJ Tobias and ML Klein Constant pressure molecular dynamics algorithms J Chem Phys 101 5 1994 with piston fluctuation control implemented using Langevin dynamics as in SE Feller Y Zhang RW Pastor and BR Brooks 85 Constant pressure molecular dynamics simulation The Langevin piston method J Chem Phys 103 11 1995 The equations of motion are r p m r p F ep gp R V 3Ve e 3V W P Po gee Re W W 3N7r kT 2mgkT h oscillationperiod ER 2WgekT h A a N V II 4 Here W is the mass of piston R is noise on atoms and Re is the noise on the piston The user specifies the desired pressure oscillation and decay times of the piston and tempera ture of the piston The compressibility of the system is not required In addition the user specifies the damping coefficients and temperature of the atoms for Langevin dynamics The following parameters are used to define the algorithm e LangevinPiston lt use Langevin piston pressure control gt Acceptable Values on or off Default Value off Description Specifies whether or not Langevin piston pressure control is ac tive If set to on then the parameters LangevinPistonTarget LangevinPistonPeriod LangevinPistonDecay and LangevinPistonTemp must be set e LangevinPistonTarget lt
240. mes rather than numbers in psf files 4 Build protein segment Actually build a segment calling it BPTI and reading the sequence of residues from the stripped pdb file created above In addition to the pdb command we could specify residues explicitly Both angles and dihedrals are generated automatically unless auto none is added which is required to build residues of water The commands first and last may be used to change the default patches for the ends of the chain The structure is built when the closing is encountered and some errors regarding the first and last residue are normal 5 Patch protein segment Some patch residues those not used to begin or end a chain are applied after the segment is built These contain all angle and dihedral terms explicitly since they were already generated In this case we apply the patch for a disulfide link three separate times 6 Read protein coordinates from PDB file The same file used to generate the sequence is now read to extract coordinates In the residue ILE the atom CD is called CD1 in the pdb file so we use pdbalias atom to define the correct name If the segment names in the pdb file match the name we gave in the segment statement then we don t need to specify it again in this case we do specify the segment so that all atoms in the pdb file must belong to the segment 7 Build water segment Build a segment for the crystal waters The residue type for wa
241. meter 83 loweAndersenRate parameter 83 loweAndersenTemp parameter 83 lowerBoundary colvars colvar keyword 119 lower Wall colvars colvar keyword 120 lowerWallConstant colvars colvar keyword 120 main colvars distanceZ distanceXY key word 132 margin parameter 90 margin violations 88 martiniDielAllow parameter 61 martiniSwitching parameter 61 maxForce colvars abf keyword 149 maximumMove parameter 76 measure command 18 mergeCrossterms parameter 27 meridforce parameter 95 megridforcechargecol parameter 95 meridforcecol parameter 95 megridforcecontl parameter 95 meridforcecont2 parameter 96 meridforcecont3 parameter 96 meridforcefile parameter 95 meridforcelite parameter 96 megridforcepotfile parameter 95 meridforcescale parameter 95 meridforcevoff parameter 96 megridforcevolts parameter 95 minBabyStep parameter 76 minimization parameter 76 minimize command 17 minLineGoal parameter 76 min TinyStep parameter 76 MISC energy 27 molly parameter 79 mollylIterations parameter 80 mollyTolerance parameter 80 movingConstraints parameter 97 movingConsVel parameter 98 MSM parameter 53 MSMApprox parameter 54 MSMBlockSizeX MSMBlockSizeY MSM BlockSizeZ parameter 55 MSMGridSpacing parameter 54 MSMLevels parameter 55 MSMPadding parameter 55 MSMQuality parameter 54 MSMsSerial parameter 56 MSMSplit parameter 55 MSMxmax MSMymax MSMzmax parame ter 55 MSMxmin MSMymin MSMzmin param
242. minimum is canceled out by the sum of the Gaussian hill functions At that stage the the effective potential of mean force A is constant and Vineta is an accurate estimator of the real potential of mean force A save for an additive constant A Vmetal K 56 Assuming that the set of collective variables includes all relevant degrees of freedom the pre dicted error of the estimate is a simple function of the correlation times of the colvars T and of the user defined parameters W g and dt 14 In typical applications a good rule of thumb can be to choose the ratio W dt much smaller than gT Te where TE is the longest among amp s correlation times g then dictates the resolution of the calculated PMF To enable a metadynamics calculation a metadynamics block must be defined in the colvars configuration file Its only mandatory keyword is the colvars option listing all the variables involved multidimensional PMFs are obtained by the same metadynamics instance applied to all the colvars The parameters W and t are specified by the keywords hillWeight and newHillFrequency respectively The values of these options are optimal for colvars with correlation times TE in the range of a few thousand simulation steps typical of many biomolecular simulations e hillWeight lt Height of each hill kcal mol gt Context metadynamics Acceptable Values positive decimal Default Value 0
243. mmand 18 reloadCharges command 18 replica exchange 181 replicaAtomRecv command 19 replicaAtomSend command 19 replicaAtomSendrecv command 19 replicaBarrier command 19 replicaDcdFile command 19 replicaEval command 19 replicalD colvars metadynamics keyword 156 replicaRecv command 19 replicaSend command 19 replicaSendrecv command 19 replicasRegistry colvars metadynamics key word 156 replicaUniformPatchGrids parameter 19 replicaUpdateFrequency colvars metadynamics keyword 156 replicaYield command 19 rescaleFreq parameter 82 rescaleTemp parameter 17 82 rescalevels command 18 resetpsf psfgen command 42 residue psfgen command 40 residueRange colvars alpha keyword 141 restartfreq parameter 25 restartname parameter 17 25 restartsave parameter 25 rigidBonds parameter 61 rigidDieOnError parameter 62 rigidIterations parameter 61 rigidTolerance parameter 61 rotateReference colvars atom group keyword 127 rotConsAxis parameter 98 rotConsPivot parameter 99 rotConstraints parameter 98 rotConsVel parameter 99 run command 16 run norepeat command 16 runAve colvars colvar keyword 124 runAveLength colvars colvar keyword 124 runAveOutputFile colvars colvar keyword 124 runAveStride colvars colvar keyword 124 SASA parameter 71 saveFreeEnergyFile keyword 154 scnb parameter 28 scriptedColvarForces colvars global keyword 163 scriptedFunction colvars colvar keyw
244. mmands in Tcl syntax to build the primary structure of the segment including auto first last residue pdb etc Context After topology definitions and residue aliases May call multiple times Structure information is generated at the end of every segment command auto angles dihedrals none Purpose Override default settings from topology file for automatic generation of angles and dihedrals for the current segment Arguments angles Enable generation of angles from bonds dihedrals Enable generation of dihedrals from angles none Disable generation of angles and dihedrals Context Anywhere within segment does not affect later segments first lt patch name gt Purpose Override default patch applied to first residue in segment Default is read from topology file and may be residue specific Arguments lt patch name gt Single target patch residue name or none Context Anywhere within segment does not affect later segments last lt patch name gt Purpose Override default patch applied to last residue in segment Default is read from topology file and may be residue specific Arguments lt patch name gt Single target patch residue name or none Context Anywhere within segment does not affect later segments residue lt resid gt lt resname gt chain Purpose Add a single residue to the end of the current segment Arguments lt resid gt Unique name for residue 1 5 characters usually numeric lt re
245. mn indicates that the atom is not enhanced Any other value should be a positive integer less than lesFactor 12 4 Replica exchange simulations The lib replica directory contains Tcl scripts that implement replica exchange both for parallel tempering temperature exchange and umbrella sampling exchanging collective variable biases This replaces the old Tcl server and socket connections driving a separate NAMD process for every replica used in the simulation A NAMD build based on Charm 6 5 0 or later using one of the LRTS low level runtime system machine layers is required Current LRTS machine layers include mpi netlrts verbs for InfiniBand gemini_gni crayxe gni crayxc and pamilrts bluegeneq Only temperature exchange simulations are described below To employ replicas for um brella sampling you will need to understand this material collective variable based calculations Sec 10 and basic Tcl programming to adapt the examples in 1ib replica umbrella and lib replica umbrella2d until further documentation and a tutorial are available This implementation is designed to be modified to implement exchanges of parameters other than temperature or via other temperature exchange methods The scripts should provide a good starting point for any simulation method requiring a number of loosely interacting systems Replica exchanges and energies are recorded in the history files written in the output directories These can be vie
246. mol A The occupancy O serves as a scaling factor which could expand the range of the force applied One may be unable to record very large or very small numbers in the data fields of a PDB file due to limited space Zero forces are ignored Specifying consforcefile is optional constant forces may be specified or updated between runs by using the consForceConfig command e consForceScaling lt Scaling factor for constant forces gt Acceptable Values decimal Default Value 1 0 Description Scaling factor by which constant forces are multiplied May be changed between run commands 9 2 External Electric Field NAMD provides the ability to apply a constant electric field to the molecular system being simu lated Energy due to the external field will be reported in the MISC column and will be continuous even in simulations using periodic boundary conditions as unwrapped coordinates are used to cal culate energy and pressure resulting in linearly increasing pressure over time for systems with free ions To avoid this effect for periodic simulations the new eFieldNormalized option should be used with the electric field vector multiplied by the cell dimension There are three parameters that control this feature e eFieldOn lt apply electric field gt Acceptable Values yes or no Default Value no Description Specifies whether or not an electric field is applied e eField lt electric field vector gt Acceptable Values vector
247. mp will be held at this value once it has been reached This parameter is valid only if reassignIncr has been set 7 4 5 Lowe Andersen dynamics parameters NAMD can perform Lowe Andersen dynamics a variation of Andersen dynamics whereby the radial relative velocities of atom pairs are randomly modified based on a thermal distribution The Lowe Andersen thermostat is Galilean invariant therefore conserving momentum and is thus 82 independent of absolute atom velocities Forces are applied only between non bonded non hydrogen pairs of atoms When using rigid bonds forces are applied to the center of mass of hydrogen groups The implementation is based on Koopman and Lowe 42 e loweAndersen lt use Lowe Andersen dynamics gt Acceptable Values on or off Default Value off Description Specifies whether or not Lowe Andersen dynamics are active If set to on then the parameter loweAndersenTemp must be set and the parameters loweAndersenCutoff and loweAndersenRate can optionally be set e loweAndersenTemp lt temperature for Lowe Andersen calculations K gt Acceptable Values positive decimal Description Temperature of the distribution used to set radial relative velocities This determines the target temperature of the system e loweAndersenCutoff lt cutoff radius for Lowe Andersen collisions A gt Acceptable Values positive decimal Default Value 2 7 Description Forces are only applied to atoms within this distance of one
248. n of Drude oscillators gt Acceptable Values on or off Default Value off Description The integration uses a dual Langevin thermostat to freeze the Drude oscil lators while maintaining the warm degrees of freedom at the desired temperature Must also enable the Langevin thermostat If drude is set to on then drudeTemp must also be defined e drudeTemp lt temperature for freezing the Drude oscillators K gt Acceptable Values non negative decimal Description For stability the Drude oscillators must be kept at a very cold termpature Using a Langevin thermostat it is possible to set this temperature to 0 K e drudeDamping lt damping coefficient for Drude oscillators 1 ps gt Acceptable Values positive decimal Description The Langevin coupling coefficient to be applied to the Drude oscillators If not given drudeDamping is set to the value of langevinDamping e drudeBondLen lt Drude oscillator bond length beyond which to apply restraint A gt Acceptable Values positive decimal Description An additional quartic restraining potential is applied to a Drude oscilla tor if its length exceeds drudeBondLen The recommended value is 0 2 A fitted from QM calculations e drudeBondConst lt Drude oscillator restraining force constant gt Acceptable Values positive decimal Description If drudeBondConst is defined an additional quartic restraining potential is applied to a Drude oscillator if its length exceeds drudeBondLen
249. n printed intermediate steps If you print energies on every timestep you will see the effect clearly in the PRESSURE field The following options affect all pressure control methods e useGroupPressure lt group or atomic quantities gt Acceptable Values yes or no Default Value no Description Pressure can be calculated using either the atomic virial and kinetic energy the default or a hydrogen group based pseudo molecular virial and kinetic energy The latter fluctuates less and is required in conjunction with rigidBonds SHAKE e useFlexibleCell lt anisotropic cell fluctuations gt Acceptable Values yes or no Default Value no Description NAMD allows the three orthogonal dimensions of the periodic cell to fluctuate independently when this option is enabled e useConstantRatio lt constant shape in first two cell dimensions gt Acceptable Values yes or no Default Value no Description When enabled NAMD keeps the ratio of the unit cell in the x y plane constant while allowing fluctuations along all axes The useFlexibleCell option is required for this option e useConstantArea lt constant area and normal pressure conditions gt Acceptable Values yes or no Default Value no Description When enabled NAMD keeps the dimension of the unit cell in the x y plane constant while allowing fluctuations along the z axis This is not currently implemented in Berendsen s method 7 5 1 Berendsen pressure bath coupling NAMD pr
250. n starts with MD or RAMD steps ignored if pure RAMD simulation is performed Should be set to yes if initial MD steps are desired e ramd ramdSteps lt Set number steps in RAMD block gt Acceptable Values positive integer Default Value 50 Description Specifies the number of steps in 1 RAMD block the simulations are evaluated every ramdSteps steps e ramd mdSteps lt Set number steps in MD block gt Acceptable Values positive integer Default Value 0 Description Specifies the number of steps in 1 standard MD block in combined RAMD MD simulations the RAMD blocks are evaluated every ramdSteps the MD blocks every mdSteps steps Default of 0 gives pure RAMD simulation 184 ramd accel lt Set acceleration energy gt Acceptable Values positive decimal Default Value 0 25 Description Specifies acceleration in kcal mol A amu to be applied during RAMD step ramd rMinRamd lt Set threshold for distance traveled RAMD gt Acceptable Values positive decimal Default Value 0 01 Description Specifies a threshold value for the distance in Angstroms traveled by the ligand in 1 RAMD block In pure RAMD simulations the direction of the acceleration is changed if the ligand traveled less than rMinRamd Ain the evaluated block In combined RAMD MD simulations a switch from a RAMD block to a standard MD block is applied if the ligand traveled more than rMinRamd Ain the evaluated block ramd rMinMd lt S
251. namic integration TI 11 1 Theoretical Background Free energy differences can be obtained through four different routes i probability densities ii free energy perturbation iii thermodynamic integration or iv nonequilibrium work ap proaches 17 Within NAMD alchemical transformations are modeled following the second and the third routes both of which rely upon the use of a general extent parameter often referred to as the coupling parameter 8 48 39 40 for the description of chemical changes in the molecular systems between the reference and the target states 11 1 1 The dual topology paradigm In a typical alchemical transformation setup involving the alteration of one chemical species into an alternate one in the course of the simulation the atoms in the molecular topology can be classified into three groups i a group of atoms that do not change during the simulation e g the environment ii the atoms describing the reference state a of the system and iii the atoms that correspond to the target state b at the end of the alchemical transformation The atoms representative of state a should never interact with those of state b throughout the MD simulation Such a setup in which atoms of both the initial and the final states of the system are present in the molecular topology file i e the psf file is characteristic of the so called dual topology paradigm 25 57 3 The hybrid Hamiltonian of the s
252. namics method uses a history dependent potential 43 that generalizes to any type of colvars the conformational flooding 28 and local elevation 36 methods originally formulated to use as colvars the principal components of a covariance matrix or a set of dihedral angles respectively The metadynamics potential on the colvars 1 2 n is defined as U lt t Nev E ANY Vineta amp y w exp Eee 55 i 1 2 t 0t 204 20 where Vineta is the history dependent potential acting on the current values of the colvars and depends only parametrically on the previous values of the colvars Vineta is constructed as a sum of Ney dimensional repulsive Gaussian hills whose height is a chosen energy constant W and whose centers are the previously explored configurations 0t 20t Each Gaussian functions has a width of approximately 2d along the direction of the i th colvar During the simulation the system evolves towards the nearest minimum of the effective potential of mean force A which is the sum of the real underlying potential of mean force 152 A and the the metadynamics potential Vineta Therefore at any given time the probability of observing the configuration is proportional to exp Ate BT this is also the probability that a new Gaussian hill is added at that configuration If the simulation is run for a sufficiently long time each local
253. nary DCD velocity trajectory filename This file stores the trajectory of all atom velocities using the same format binary DCD as X PLOR If velDCDfile is defined then velDCDfreq must also be defined velDCDfreq lt timesteps between writing velocities to trajectory file gt Acceptable Values positive integer Description The number of timesteps between the writing of velocities to the trajectory file The initial velocities will not be included in the trajectory file Velocities in DCD files are stored in NAMD internal units and must be multiplied by PDBVELFACTOR 20 45482706 to convert to A ps forceDCDfile lt force trajectory output file gt Acceptable Values UNIX filename Default Value outputname forcedcd Description The binary DCD force trajectory filename This file stores the trajectory of all atom forces using the same format binary DCD as X PLOR If forceDCDfile is defined then forceDCDfreq must also be defined forceDCDfreq lt timesteps between writing force to trajectory file gt Acceptable Values positive integer Description The number of timesteps between the writing of forces to the trajectory file The initial forces will not be included in the trajectory file Forces in DCD files are stored in kcal mol A In the current implementation only those forces that are evaluated during the timestep that a frame is written are included in that frame This is different from the behavior of TclForces and is likely to c
254. nation number calculated between atoms 1 to 10 and atoms 11 to 20 A harmonic restraint is applied to both d and c to allow using the same force constant K both d and c are scaled by their respective fluctuation widths wg and we A third colvar alpha is defined as the a helical content of residues 1 to 10 The values of c and alpha are also recorded throughout the simulation as a joint 2 dimensional histogram e colvars lt Enable the collective variables module gt Context NAMD configuration file Acceptable Values boolean Default Value off Description If this flag is on the collective variables module within NAMD is enabled the module requires a separate configuration file to be provided with colvarsConfig e colvarsConfig lt Configuration file for the collective variables gt Context NAMD configuration file Acceptable Values UNIX filename Description This file contains the definition of all collective variables and their biasing or analysis methods Parameters within the configuration file can be controlled from a NAMD config file using Tcl variables in the following way colvars on colvarsConfig colvars_subst tmp set myParameter someValue 114 Parse template and create specific config file on the fly set infile open colvars_template in r set outfile open colvars_subst tmp wt puts outfile subst read infile close infile close outfile In this example the string myParameter will be re
255. nce at which the switching function should start taking effect to bring the van der Waals potential to O smoothly at the cutoff distance Thus the value of switchdist must always be less than that of cutoff 5 2 2 Electrostatic interactions The handling of electrostatics is slightly more complicated due to the incorporation of multiple timestepping for full electrostatic interactions There are two cases to consider one where full electrostatics is employed and the other where electrostatics are truncated at a given distance First let us consider the latter case where electrostatics are truncated at the cutoff distance Using this scheme all electrostatic interactions beyond a specified distance are ignored or assumed to be zero If switching is set to on rather than having a discontinuity in the potential at the cutoff distance a shifting function is applied to the electrostatic potential as shown in Figure 2 As this figure shows the shifting function shifts the entire potential curve so that the curve intersects the x axis at the cutoff distance This shifting function is based on the shifting function used by X PLOR Next consider the case where full electrostatics are calculated In this case the electrostatic interactions are not truncated at any distance In this scheme the cutoff parameter has a slightly different meaning for the electrostatic interactions it represents the local interaction distance or distance within which el
256. nciple be done through a TclForces script using the colvars module is both easier and computationally more efficient e calculate potentials of mean force PMFs along any set of colvars using different enhanced sampling methods such as Adaptive Biasing Force ABF metadynamics steered MD and umbrella sampling variants of these methods that make use of an ensemble of replicas are supported as well e calculate statistical properties of the colvars such as running averages and standard devia tions correlation functions of pairs of colvars and multidimensional histograms this can be done either at run time without the need to save very large trajectory files or after a sim ulation has been completed using VMD and the cv command or NAMD and the coorfile read command as illustrated in 16 To briefly illustrate the flexibility of the colvars module Figure 6 shows an example of a non trivial configuration the corresponding input can be found in 10 1 2 Detailed explanations of the design of the colvars module are provided in reference 23 Please cite this reference whenever publishing work that makes use of this module 10 1 General parameters and input output files Here we document the syntax of the commands and parameters used to set up and use the collective variables module in NAMD One of these parameters is the configuration file or the configuration text for the module itself whose syntax is described in 10 1 2 and in the fol
257. nd D G Truhlar Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium J Phys Chem 100 19824 19839 1996 J H nin and C Chipot Overcoming free energy barriers using unconstrained molecular dynamics simulations J Chem Phys 121 2904 2914 2004 J H nin G Fiorin C Chipot and M L Klein Exploring multidimensional free energy landscapes using time dependent biases on collective variables J Chem Theory Comput 6 1 35 47 2010 T Huber A E Torda and W van Gunsteren Local elevation A method for improving the searching properties of molecular dynamics simulation Journal of Computer Aided Molecular Design 8 6 695 708 DEC 1994 M lannuzzi A Laio and M Parrinello Efficient exploration of reactive potential energy surfaces using car parrinello molecular dynamics Phys Rev Lett 90 23 238302 2003 W Jiang D Hardy J Phillips A MacKerell K Schulten and B Roux High performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD J Phys Chem Lett 2 87 92 2011 P M King Free energy via molecular simulation A primer In W F Van Gunsteren P K Weiner and A J Wilkinson editors Computer simulation of biomolecular systems Theoretical and experimental applications volume 2 pages 267 314 ESCOM Leiden 1993 J G Kirkwood Statistical mec
258. nd dG is restarted The accumulated net free energy change is written at each lambda value and at the end of the simulation Whereas the FEP module of NAMD supplies free energy differences determined from equa tion 59 the wealth of information available in alchOutFile may be utilized profitably to explore different routes towards the estimation of AA Both BAR and SOS methods which combine advantageously direct and reverse transformations to improve convergence and accuracy of the calculation represent relevant alternatives to brute force application of the FEP formula 46 Within the SOS framework the free energy difference between states A and A 41 is expressed as exp E H x Pa Acta HS Pos anit exp 1 5 H x Po Ai H X Pz aanl and can be readily used with the statistical information provided by the forward and the backward ep AA i 62 14 1 runs 11 4 2 Thermodynamic Integration When running TI free energy calculations the elec_dU dl and vdW_dU dl1 values reported in ti0utFile are the derivatives of the internal energy with respect to A i e ae for electro statics and van der Waals respectively dU d1 values are averages over the last tiOutFreq steps Cumulative averages for each component are reported alongside in the _avg columns The electrostatics and vdW are separated following a partition scheme that is the appear ing and the disappearing atoms are accounted for separately
259. ndaries and widths saved in the state file override those in the configuration file Enabling this option forces the grids to match those in the current configuration file Well tempered metadynamics The following options define the configuration for the well tempered metadynamics approach 4 e wellTempered lt Perform well tempered metadynamics gt Context metadynamics Acceptable Values boolean Default Value off Description If enabled this flag causes well tempered metadynamics as described by Barducci et al 4 to be performed rather than standard metadynamics The parameter biasTemperature is then required This feature was contributed by Li Li Luthey Schulten group Departement of Chemistry UIUC e biasTemperature lt Temperature bias for well tempered metadynamics gt Context metadynamics Acceptable Values positive decimal Description When running metadynamics in the long time limit collective variable space is sampled to a modified temperature T AT In conventional metadynamics the temperature boost AT would constantly increases with time Instead in well tempered metadynamics AT must be defined by the user via biasTemperature If dumpFreeEnergyFile is enabled the written PMF includes the scaling factor T AT AT 4 A careful choice of AT determines the sampling and convergence rate and is hence crucial to the success of a well tempered metadynamics simulation Multiple replicas metadynamics The fol
260. ng overlap of unbounded electrostatic poten tials consists of allowing a bounded soft core vdW potential using a positive value of alchVdWShiftCoeff to repel first all overlapping particles at low values of A As A increases once the particles are repelled it becomes safe to turn on FEP or TI electrostatics 169 Decoupling Mutation elecLambdaStart 0 5 vdwLambdaEnd 1 0 elecLambdaStart 0 5 vdwLambdaEnd 0 7 ale o LEF o 2 2 w F Ss gt gt 0 4 A 0 2 0 fe esl Se 0 E 3 0 02 04 06 08 1 0 02 04 06 08 1 A user controlled A user controlled Figure 9 Relationship of user defined A to coupling of electrostatic or vdW interactions to a simulation given specific values of alchElecLambdaStart or alchVdwLambdaEnd In the current implementation the electrostatic interactions of an exnihilated or appearing particle are linearly coupled to the simulation over the A value range of alchElecLambdaStart 1 0 At A values less than or equal to the user defined value of alchElecLambdaStart electrostatic interactions of the exnihilated particle are fully decoupled from the simulation Coupling of electrostatic interactions then increases linearly for increasing values of A until A 1 0 at which point electrostatic interactions of the exnihilated particle are fully coupled to the simulation For annihilated or vanishing particles the electrostatic interactions are linearly decoupled from th
261. nge nonbonded forces every 2 fs and long range electrostatics every 4 fs e MTSAlgorithm lt MTS algorithm to be used gt Acceptable Values impulse verletI or constant naive Default Value impulse Description Specifies the multiple timestep algorithm used to integrate the long and short range forces impulse verletI is the same as r RESPA constant naive is the stale force extrapolation method e longSplitting lt how should long and short range forces be split gt Acceptable Values c1 c2 Default Value c1 Description Specifies the method used to split electrostatic forces between long and short range potentials The c1 option uses a cubic polynomial splitting function 3 r 1 r 3 Sa r 2 2 to affect C continuity in the splitting of the electrostatic potential 66 The c2 option uses a quintic polynomial splitting function ma 3 ae 4 r 5 Te Y a to affect C continuity in the splitting of the electrostatic potential The S splitting func tion contributed by Bruce Berne Ruhong Zhou and Joe Morrone produces demonstrably better long time stability than S3 without requiring any additional computational cost during simulation since the nonbonded forces are calculated via a lookup table Note that earlier options xplor and sharp are no longer supported e molly lt use mollified impulse method MOLLY gt Acceptable Values on or off Default Value off Description This method eliminates the component
262. ngs max 4 characters Description This option sets the PSF segment identifier for atomNameResidueRange Multiple values may be provided which correspond to multiple instances of atomNameResidueRange in the order of their occurrence This option is only necessary if a PSF topology file is used atomsFile lt PDB file name for atom selection gt Context atom group Acceptable Values UNIX filename Description This option selects atoms from the PDB file provided and adds them to the group according to numerical flags in the column atomsCol Note the sequence of atoms in the PDB file provided must match that in the system s topology atomsCol lt PDB column to use for atom selection flags gt Context atom group Acceptable Values 0 B X Y or Z Description This option specifies which PDB column in atomsFile is used to determine which atoms are to be included in the group atomsColValue lt Atom selection flag in the PDB column gt Context atom group Acceptable Values positive decimal Description If defined this value in atomsCol identifies atoms in atomsFile that are included in the group If undefined all atoms with a non zero value in atomsCol are included 126 e dummyAtom lt Dummy atom position A gt Context atom group Acceptable Values x y z triplet Description Instead of selecting any atom this option makes the group a virtual particle at a fixed position in space This is useful e g to replac
263. ngs need to be fixed 206 17 7 SGI Altix UV Use Linux x86_64 multicore and the following script to set CPU affinity namd2 setcpuaffinity numactl show awk physcpubind printf p d pemap d NF 1 2 for i 3 i lt NF 1i printf 7 d i For runs on large numbers of cores you will need to experiment use the following to enable the Charm communication thread namd2 setcpuaffinity numactl show awk physcpubind printf p d pemap d NF 2 2 for i 3 i lt NF i printf d i print commthread commap NF 17 8 IBM POWER Clusters Run the MPI version of NAMD as you would any POE program The options and environment variables for poe are various and arcane so you should consult your local documentation for rec ommended settings As an example to run on Blue Horizon one would specify poe namd2 lt configfile gt nodes lt procs 8 gt tasks_per_node 8 17 9 CPU Affinity NAMD may run faster on some machines if threads or processes are set to run on or not run on specific processor cores or hardware threads On Linux this can be done at the process level with the numactl utility but NAMD provides its own options for assigning threads to cores This feature is enabled by adding setcpuaffinity to the namd2 command line which by itself will cause NAMD really the underlying Charm library to assign threads processes round robin to available cores in the ord
264. ntext inertiaZ Acceptable Values x y z triplet Default Value 0 0 0 0 1 0 Description The three components of this vector define when normalized the projection axis e 139 orientation orientation from reference coordinates The block orientation re turns the same optimal rotation used in the rmsd component to superimpose the coordinates x t onto a set of reference coordinates py Such component returns a four dimensional vector q qo q1 q2 43 with gt q 1 this quaternion expresses the optimal rotation x t gt xe according to the formalism in reference 19 The quaternion qo q1 42 q3 can also be written as cos 2 sin 0 2 u where is the angle and u the normalized axis of rotation for example a rotation of 90 around the z axis is expressed as 0 707 0 0 0 0 0 707 The script quaternion2rmatrix tcl provides Tcl functions for converting to and from a 4 x 4 rotation ma trix in a format suitable for usage in VMD As for the component rmsd the available options are atoms refPositionsFile refPositionsCol and refPositionsColValue and refPositions Note refPositions and refPositionsFile define the set of positions from which the optimal rotation is calculated but this rotation is not applied to the coordinates of the atoms involved it is used instead to define the variable itself e closestToQuaternion lt Reference rotation gt Context orientation Acceptable Values q0
265. o the origin providing hexagonal or other cell shapes 7 1 2 Spherical harmonic boundary conditions NAMD provides spherical harmonic boundary conditions These boundary conditions can consist of a single potential or a combination of two potentials The following parameters are used to define these boundary conditions e sphericalBC lt use spherical boundary conditions gt Acceptable Values on or off Default Value off Description Specifies whether or not spherical boundary conditions are to be applied to the system If set to on then sphericalBCCenter sphericalBCri and sphericalBCk1 must be defined and sphericalBCexp1 sphericalBCr2 sphericalBCk2 and sphericalBCexp2 can optionally be defined e sphericalBCCenter lt center of sphere A gt Acceptable Values position Description Location around which sphere is centered e sphericalBCri lt radius for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect This distance is a radius from the center e sphericalBCk1 lt force constant for first potential gt Acceptable Values non zero decimal 73 Description Force constant for the first harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center e sphericalBCexp1 lt exponent for first potential gt Acceptable Values positive even integer
266. oard of Trustees of the University of Illinois All Rights Reserved NAMD Molecular Dynamics Software Non Exclusive Non Commercial Use License Introduction The University of Illinois at Urbana Champaign has created its molecular dynamics software NAMD developed by the Theoretical and Computational Biophysics Group TCBG at Tlli nois Beckman Institute available free of charge for non commercial use by individuals academic or research institutions and corporations for in house business purposes only upon completion and submission of the online registration form presented when attempting to download NAMD at the web site http www ks uiuc edu Research namd Commercial use of the NAMD software or derivative works based thereon REQUIRES A COMMERCIAL LICENSE Commercial use includes 1 integration of all or part of the Software into a product for sale lease or license by or on behalf of Licensee to third parties or 2 distribution of the Software to third parties that need it to commercialize product sold or licensed by or on behalf of Licensee The University of Illinois will negotiate commercial use licenses for NAMD upon request These requests can be directed to namd ks uiuc edu Online Download Registration Requirements In completing the online registration form presented before downloading individuals may register in their own name or with their institutional or corporate affiliations Registration information must inclu
267. of decimals x y z Description Vector which describes the electric field to be applied Units are 92 kcal mol e which is natural for simulations This parameter may be changed between run commands allowing a square wave or other approximate wave form to be applied eFieldNormalized lt electric field vector scaled by cell basis vectors gt Acceptable Values yes or no Default Value no Description Specifies whether or not that eField vector has been scaled by the cell basis vectors thus indicating the voltage drop across the cell in units of kcal mol e The eField vector is then scaled by the reciprocal lattice vectors at each timestep When eFieldNormal ized is true the eField forces do not contribute to the pressure calculation 9 3 Grid Forces NAMD provides the ability to specify grids describing a potential in the simulation space Each atom is affected by the potential based on its charge and its position using the potential function interpolated from the specified grid s Energy due to the grid defined field will be reported in the MISC column of the output unless a scaling factor not proportional to 1 1 1 is used NAMD allows the definition of multiple grids each with a separate set of defining parame ters This is specified using a tag field in each of the mgridforceXXX commands The tag is an alphanumeric string without spaces which identifies to which grid the specified field applies The grid file forma
268. of itself on other nodes and to provide access to a high performance network such as Myrinet or InfiniBand if one is available For typical workstations Windows Linux Mac OS X or other Unix with only ethernet net working hopefully gigabit NAMD uses the Charm native communications layer and the pro gram charmrun to launch namd2 processes for parallel runs either exclusively on the local machine with the local option or on other hosts as specified by a nodelist file The namd2 binaries for these platforms can also be run directly known as standalone mode for single process runs 17 1 Individual Windows Linux Mac OS X or Other Unix Workstations Individual workstations use the same version of NAMD as workstation networks but running NAMD is much easier If your machine has only one processor core you can run the any non MPI namd2 binary directly namd2 lt configfile gt Windows Mac OX X Intel and Linux x86_64 multicore released binaries are based on mul ticore builds of Charm that can run multiple threads These multicore builds lack a network layer so they can only be used on a single machine For best performance use one thread per processor with the p option namd2 p lt procs gt lt configfile gt For other multiprocessor workstations the included charmrun program is needed to run multiple namd2 processes The local option is also required to specify that only the local machine is being used charmrun
269. olvars of arbitrary size Calculating system forces In addition to the restrictions due to the type of value computed scalar or non scalar a final restriction can arise when calculating system force outputSystemForce option or application of a abf bias System forces are available currently only for the following components distance distanceZ distanceXY angle dihedral rmsd eigenvector and gyration 144 10 4 3 Linear and polynomial combinations of components To extend the set of possible definitions of colvars r multiple components q r can be summed with the formula El So alale 48 2 where each component appears with a unique coefficient c 1 0 by default the positive integer exponent n 1 by default Any set of components can be combined within a colvar provided that they return the same type of values scalar unit vector vector or quaternion By default the colvar is the sum of its components Linear or polynomial combinations following equation 48 can be obtained by setting the following parameters which are common to all components e componentCoeff lt Coefficient of this component in the colvar gt Context any component Acceptable Values decimal Default Value 1 0 Description Defines the coefficient by which this component is multiplied after being raised to componentExp before being added to the sum e componentExp lt Exponent of this component in the colvar gt Context any com
270. om should not be constrained Otherwise the value specified is used as the force constant for that atom s restraining potential 62 e constraintScaling lt scaling factor for harmonic constraint energy function gt Acceptable Values positive Default Value 1 0 Description The harmonic constraint energy function is multiplied by this parameter making it possible to gradually turn off constraints during equilibration This parameter is used only if constraints is set to on e selectConstraints lt Restrain only selected Cartesian components of the coordinates gt Acceptable Values on or off Default Value off Description This option is useful to restrain the positions of atoms to a plane or a line in space If active this option will ensure that only selected Cartesian components of the coordinates are restrained E g Restraining the positions of atoms to their current z values with no restraints in x and y will allow the atoms to move in the x y plane while retaining their original z coordinate Restraining the x and y values will lead to free motion only along the z coordinate e selectConstrX lt Restrain X components of coordinates gt Acceptable Values on or off Default Value off Description Restrain the Cartesian x components of the positions e selectConstrY lt Restrain Y components of coordinates gt Acceptable Values on or off Default Value off Description Restrain the Cartesian y components of the positions
271. on flags gt Acceptable Values filename Default Value coordinates Description pdb file to be used for indicating the status of all atoms pertaining to the 168 system with respect to the alchemical transformation If this parameter is not declared specifically then the pdb file specified by coordinates is utilized for this information alchCol lt Column in the alchFile that carries the perturbation flag gt Acceptable Values X Y Z O or B Default Value B Description Column of the pdb file to use for retrieving the status of each atom i e a flag that indicates which atom will be perturbed in the course of the alchemical transformation A value of 1 in the specified column indicates that the atom will vanish as A moves from 0 to 1 whereas a value of 1 indicates that it will grow alchOutFreq lt Frequency of free energy output in time steps gt Acceptable Values positive integer Default Value 5 Description Every alchOutFreq number of MD steps the output file alchOutFile is updated by dumping energies that are used for ensemble averaging This variable could be set to 1 to include all the configurations for ensemble averaging Yet it is recommended to update alchOutFile energies at longer intervals to avoid large files containing highly correlated data unless a post treatment e g Bennett s acceptance ratio BAR 5 or simple overlap sampling SOS 46 is to be performed alchOutFile lt Alchemical free energ
272. on in NAMD may be viewed and altered with VMD for instance forces can be applied to a set of atoms to alter or rearrange part of the molecular structure For more information on VMD see http www ks uiuc edu Research vmd e Load Balancing An important factor in parallel applications is the equal distribution of computational load among the processors In parallel molecular simulation a spatial decomposition that evenly distributes the computational load causes the region of space mapped to each processor to become very irregular hard to compute and difficult to generalize to the evaluation of many different types of forces NAMD addresses this problem by using a simple uniform spatial decomposition where the entire model is split into uniform cubes of space called patches An initial load balancer assigns patches and the calculation of interactions among the atoms within them to processors such that the computational load is balanced as much as possible During the simulation an incremental load balancer monitors the load and performs necessary adjustments 1 2 Acknowledgments NAMD development is supported by the National Institutes of Health NIH 9P41GM104601 and relies on computational resources funded by the National Science Foundation and the Department of Energy The authors would particularly like to thank the members of the Theoretical and Computational Biophysics Group past and present who have helped tremendously in making sugge
273. or between two groups The distanceVec block defines a distance vector component which accepts the same keywords as the component distance groupl group2 and forceNoPEC Its value is the 3 vector joining the centers of mass of group1 and group2 distanceDir distance unit vector between two groups The distanceDir block defines a distance unit vector component which accepts the same keywords as the component distance group1 group2 and forceNoPBC It returns a 3 dimensional unit vector d dz dy dz with d 1 distanceInv mean distance between two groups of atoms The distanceInv block defines a generalized mean distance between two groups of atoms 1 and 2 weighted with exponent 1 n 1 n n 1 1 K dia Ni No za rar 36 ij where d is the distance between atoms i and j in groups 1 and 2 respectively and n is an even integer This component accepts the same keywords as the component distance group1 group2 and forceNoPBC In addition the following option may be provided e exponent lt Exponent n in equation 36 gt Context distancelnv Acceptable Values positive even integer Default Value 6 Description Defines the exponent to which the individual distances are elevated before 133 averaging The default value of 6 is useful for example to applying restraints based on NOE measured distances This component returns a number in A ranging from 0 to the largest possible distance wit
274. or excluded and 0 for not excluded ExcludeFromPressureCol lt Column in PDB file for specifying excluded atoms gt Acceptable Values O B X Y or Z Default Value O Description Specifies which column of the pdb file to check for excluded atoms 87 8 Performance Tuning 8 1 Non bonded interaction distance testing The last critical parameter for non bonded interaction calculations is the parameter pairlistdist To reduce the cost of performing the non bonded interactions NAMD uses a non bonded pair list which contained all pairs of atoms for which non bonded interactions should be calculated Per forming the search for pairs of atoms that should have their interactions calculated is an expensive operation Thus the pair list is only calculated periodically at least once per cycle Unfortunately pairs of atoms move relative to each other during the steps between preparation of the pair list Because of this if the pair list were built to include only those pairs of atoms that are within the cutoff distance when the list is generated it would be possible for atoms to drift closer to gether than the cutoff distance during subsequent timesteps and yet not have their non bonded interactions calculated Let us consider a concrete example to better understand this Assume that the pairlist is built once every ten timesteps and that the cutoff distance is 8 0 Consider a pair of atoms A and B that are 8 1 apart when the pairlist is
275. orce lt fx gt lt fy gt lt fz gt Adds the specified force to the current atom for this step e addenergy lt energy gt Adds potential energy to the BOUNDARY column of NAMD output As an example these spherical boundary condition forces sphericalBC on sphericalBCcenter 0 0 0 0 0 0 sphericalBCri 48 sphericalBCk1 10 sphericalBCexp1 2 110 Are replicated in the following script tc1BC on tclBCScript proc veclen2 vi foreach x1 y1 z1 v1 break return expr x1 x1 y1x y1 z1 z1 wrapmode input wrapmode cell wrapmode nearest wrapmode patch the default H proc calcforces step unique R K if step 20 0 cleardrops if unique print clearing dropped atom list at step step set R expr 1 R set R2 expr R R set tol 2 0 set cut2 expr R tol R tol while nextatom addenergy 1 monitor how many atoms are checked set rvec getcoord set r2 veclen2 rvec if r2 lt cut2 dropatom continue if r2 gt R2 addenergy 1 monitor how many atoms are affected set r expr sqrt r2 addenergy expr K r R r R addforce vecscale rvec expr 2 K r R r tclBCArgs 48 0 10 0 111 9 12 External Program Forces This feature allows an external program to be called to calculate forces at every force evaluation taking all atom coordinates as input e extForces lt Apply external program forces gt A
276. orces This commonality allows simulations to migrate between these three programs e Efficient Full Electrostatics Algorithms NAMD incorporates the Particle Mesh Ewald PME algorithm which takes the full elec trostatic interactions into account This algorithm reduces the computational complexity of electrostatic force evaluation from O N to O N log N e Multiple Time Stepping The velocity Verlet integration method 1 is used to advance the positions and velocities of the atoms in time To further reduce the cost of the evaluation of long range electrostatic forces a multiple time step scheme is employed The local interactions bonded van der Waals and electrostatic interactions within a specified distance are calculated at each time step The longer range interactions electrostatic interactions beyond the specified distance are only computed less often This amortizes the cost of computing the electrostatic forces over several timesteps A smooth splitting function is used to separate a quickly varying short range portion of the electrostatic interaction from a more slowly varying long range component It is also possible to employ an intermediate timestep for the short range non bonded interactions performing only bonded interactions every timestep e Input and Output Compatibility The input and output file formats used by NAMD are identical to those used by CHARMM and X PLOR Input formats include coordinate files in PDB format 6
277. ord 145 scriptedFunctionType colvars colvar key word 146 scriptedFunctionVectorSize colvars keyword 146 seed parameter 77 segment psfgen command 40 selectConstraints parameter 63 selectConstrX parameter 63 selectConstrY parameter 63 selectConstrZ parameter 63 shared colvars abf keyword 150 sharedFreq colvars abf keyword 151 SMD parameter 104 SMDDir parameter 104 SMDFile parameter 104 SMDk parameter 104 S S S colvars metadynamics colvar MDk2 parameter 104 MDOutputFreq parameter 104 MDVel parameter 104 solventDielectric parameter 70 source command 16 sphericalBC parameter 73 sphericalBCCenter parameter 73 sphericalBCexp1 parameter 74 sphericalBCexp2 parameter 74 sphericalBCk1 parameter 73 sphericalBCk2 parameter 74 sphericalBCrl1 parameter 73 sphericalBCr2 parameter 74 splitPatch parameter 90 startup command 17 staticAtomAssignment parameter 190 stepspercycle parameter 90 StrainRate parameter 87 225 structure parameter 23 surfaceTension parameter 71 SurfaceTensionTarget parameter 17 87 switchdist parameter 50 switching parameter 49 symmetryFile parameter 100 symmetryFirstFullStep parameter 99 symmetryFirstStep parameter 100 symmetryk parameter 99 symmetrykFile parameter 99 symmetryLastFullStep parameter 99 symmetryLastStep parameter 101 symmetryMatrixFile parameter 100 symmetryRestraints parameter 99 symmetryScaleForces parameter 100 table
278. output gt se sesa doa a a na Ae ea a ee 5 4 3 Drude force field parameters oaoa a a a a MARTINI Residue Based Coarse Grain Forcefield oo a a a Constraints and Restraints a 5 6 1 Bond constraint parameters 5 6 2 Harmonic restraint parameters a 5 6 3 Fixed atoms parameters 5 6 4 Extra bond angle and dihedral restraints Generalized Born Implicit Solvent Theoretical Background ee ee 6 1 1 Poisson Boltzmann Equation 0 000002 eee eee 6 1 2 Generalized Bori li Ret Boe hate Was a he ne a dp 6 1 3 Generalized Born Equations 0 0 000002 eee ee eee 3 Phase Calculation e ea a E a o a a a a e a a e a a a a A Configuration Parameters a Standard Minimization and Dynamics Parameters Boundary Conditigns s ci ea se eA Pe eek cod 7 1 1 Periodic boundary conditions 2 e 7 1 2 Spherical harmonic boundary conditions 7 1 3 Cylindrical harmonic boundary conditions Energy Minimization ee 7 2 1 Conjugate gradient parameters 2 20 0 0 e 7 2 2 Velocity quenching parameters 2 e a Dynamics inte isles 40 it ahs he ah be gh ow Rok wees Why ee te ke ae ee RA 7 3 1 Timestep parameters satie ao e e p ehi e e e e E a e a e au oTe S T32 Initialization a a ol ee a Di Be 7 3 3 Conserving momentum 0 0002 eee ee ee 7 3 4 Multiple timestep parameters Temperature
279. ovides constant pressure simulation using Berendsen s method The following parameters are used to define the algorithm e BerendsenPressure lt use Berendsen pressure bath coupling gt Acceptable Values on or off 84 Default Value off Description Specifies whether or not Berendsen pressure bath coupling is active If set to on then the parameters BerendsenPressureTarget BerendsenPressureCompressibility and BerendsenPressureRelaxationTime must be set and the parameter BerendsenPressureFreq can optionally be set to control the behavior of this feature BerendsenPressureTarget lt target pressure bar gt Acceptable Values positive decimal Description Specifies target pressure for Berendsen s method A typical value would be 1 01325 bar atmospheric pressure at sea level BerendsenPressureCompressibility lt compressibility bar gt Acceptable Values positive decimal Description Specifies compressibility for Berendsen s method A typical value would be 4 57E 5 bar corresponding to liquid water The higher the compressibility the more volume will be adjusted for a given pressure difference The compressibility and the relaxation time appear only as a ratio in the dynamics so a larger compressibility is equivalent to a smaller relaxation time BerendsenPressureRelaxationTime lt relaxation time fs gt Acceptable Values positive decimal Description Specifies relaxation time for Berendsen s method If the
280. owerWall lt Position of the lower wall gt Context colvar Acceptable Values decimal Default Value lowerBoundary Description Defines the value below which a confining restraint on the colvar is applied in the form of a half harmonic potential Allows to use a different position of the wall than lowerBoundary e upperWallConstant lt Upper wall force constant kcal mol U gt Context colvar 120 Acceptable Values positive decimal Description Analogous to lowerWallConstant upperWall lt Position of the upper wall gt Context colvar Acceptable Values decimal Default Value upperBoundary Description Analogous to lowerWall 10 2 3 Trajectory output outputValue lt Output a trajectory for this colvar gt Context colvar Acceptable Values boolean Default Value on Description If colvarsTrajFrequency is non zero the value of this colvar is written to the trajectory file every colvarsTrajFrequency steps in the column labeled lt name gt outputVelocity lt Output a velocity trajectory for this colvar gt Context colvar Acceptable Values boolean Default Value off Description If colvarsTrajFrequency is defined the finite difference calculated velocity of this colvar are written to the trajectory file under the label v_ lt name gt outputEnergy lt Output an energy trajectory for this colvar gt Context colvar Acceptable Values boolean Default Value off Description This
281. parameter ionConcentration lt concentration of ions in solvent Molar gt Acceptable Values positive decimal Default Value 0 2 Description An ion concentration of 0 M represents distilled water Increasing the ion concentration increases the electrostatic screening GBISDelta lt GB parameter for calculating Born radii gt Acceptable Values decimal Default Value 1 0 Description Use GBISDelta GBISBeta GBISGamma 1 0 0 8 4 85 for GBOPCIL and 0 8 0 0 2 90912 for GB CT See a 3 y in 56 for more information GBISBeta lt GB parameter for calculating Born radii gt Acceptable Values decimal Default Value 0 8 Description See GBISDelta GBISGamma lt GB9PC parameter for calculating Born radii gt Acceptable Values decimal Default Value 4 85 Description See GBISDelta 70 e alphaCutoff lt cutoff used in calculating Born radius and derivatives phases 1 and 3 A gt Acceptable Values positive decimal Default Value 15 Description Cutoff used for calculating Born radius Only atoms within this cutoff de screen an atom Though alphaCutoff can bet set to be larger or shorter than cutoff since atom forces are more sensitive to changes in position than changes in Born radius user s should generally set alphaCutoff to be shorter than cutoff e SASA lt whether or not to calculate SASA gt Acceptable Values on or off Default Value off Description The nonpolar hydrophobic en
282. path including s or d for separate directo ries as in output s fold_alanin job1 This will be extended with d dcd d history for input files and d sort ded d sort history for output files The optional final step parameter will truncate all output files after the specified step which is useful in dealing with restarts from runs that did not complete Colvars trajectory files are similarly processed if they are found A replica exchange config file should define the following Tcl variables e num_replicas the number of replica simulations to use e min temp the lowest replica target temperature e max_temp the highest replica target temperature e steps_per_run the number of steps between exchange attempts e num_runs the number of runs before stopping should be divisible by runs_per_frame x frames_per_restart e runs per frame the number of runs between trajectory outputs e frames_per_restart the number of frames between restart outputs e namd_config file the NAMD config file containing all parameters needed for the sim ulation except seed langevin langevinTemp outputEnergies outputname dcdFreq temperature bincoordinates binvelocities or extendedSystem which are provided by replica namd e output_root the directory fileroot for output files optionally including a s that is re placed with the replica index to use multiple output directories e psf_file the psf file for show_replicas vmd e in
283. pdbalias residue HOH TIP3 formerly alias residue segment SOLV auto none pdb output 6PTI_water pdb 8 Read water coordinaes from PDB file pdbalias atom HOH 0 0H2 formerly alias atom coordpdb output 6PTI_water pdb SOLV 9 Guess missing coordinates guesscoord 10 Write structure and coordinate files writepsf output bpti psf writepdb output bpti pdb End of psfgen commands ENDMOL Step by step explanation of the script 1 Split input PDB file into segments 6PTI pdb is the original file from the Protein Data Bank It contains a single chain of protein and some PO4 and H20 HETATM records Since each segment must have a separate input file we remove all non protein atom records using grep If there were multiple chains we would have to split the file by hand Create a second file containing only waters 2 Embed the psfgen commands in this script Run the psfgen program taking everything until ENDMOL as input You may run psfgen interactively as well Since psfgen is built on a Tcl interpreter you may use loops variables etc but you must use for variables when inside a shell script If you want run psfgen and enter the following commands manually 35 3 Read topology file Read in the topology definitions for the residues we will create This must match the parameter file used for the simulation as well Multiple topology files may be read in since psfgen and NAMD use atom type na
284. placed with the value someValue wherever it appears in the file colvars_template in This value will then be read in by the colvars module when it parses its input colvarsInput lt Input state file for the collective variables gt Context NAMD configuration file Acceptable Values UNIX filename Description When continuing a previous simulation run this file contains the current state of all collective variables and of their associated algorithms It is written automatically at the end of any simulation with collective variables 10 1 2 Configuration syntax for the collective variables module All the parameters defining the colvars and their biasing or analysis algorithms are read from the file specified by colvarsConfig Hence none of the keywords described in this section and the following ones are available as keywords for the NAMD configuration file The syntax of the colvars configuration is keyword value where the keyword and its value are separated by any white space The following rules apply keywords are case insensitive upperBoundary is the same as upperboundary and UPPERBOUNDARY their string values are however case sensitive e g file names a long value or a list of multiple values can be distributed across multiple lines by using curly braces and the opening brace must occur on the same line as the keyword following a space character or other white space the closing brace can b
285. ponent Acceptable Values integer Default Value 1 Description Defines the power at which the value of this component is raised before being added to the sum When this exponent is different than 1 non linear sum system forces and the Jacobian force are not available making the colvar unsuitable for ABF calculations Example To define the average of a colvar across different parts of the system simply define within the same colvar block a series of components of the same type applied to different atom groups and assign to each component a componentCoeff of 1 N 10 4 4 Colvars as scripted functions of components In contexts that support scripting a colvar may be defined as custom scripted function of the values of its components rather than a linear or polynomial combination When implementing generic functions of Cartesian coordinates rather than functions of existing components the cartesian component may be particularly useful An example of elaborate scripted colvar is given in example 10 in the form of path based collective variables as defined by Branduardi et al 11 The required Tcl procedures are provided in the colvartools directory e scriptedFunction lt Compute colvar as a scripted function of its components gt Context colvar Acceptable Values string Description If this option is specified the colvar will be computed as a scripted function of the values of its components To that effect the user should define two
286. potential term Emin lt 0 which means that Emin is the well depth The Lennard Jones potential approaches 0 rapidly as r j increases so it is usually truncated smoothly shifted to 0 past a cutoff radius requiring O N computational cost The electrostatic potential is repulsive for atomic charges with the same sign and attractive for atomic charges with opposite signs Uys Emin CEQ Uelec 14 e gt 7 EOTij where ri r Fil gives the distance between the pair of atoms and q and q are the charges on the respective atoms Coulomb s constant C and the dielectric constant ey are fixed for all electrostatic interactions The parameter 14 is a unitless scaling factor whose value is 1 except for a modified 1 4 interaction where the pair of atoms is separated by a sequence of three covalent bonds so that the atoms might also be involved in a torsion angle interaction in which case 14 for a fixed constant 0 lt lt 1 Although the electrostatic potential may be computed with a cutoff like the Lennard Jones potential the 1 r potential approaches 0 much more slowly than the 1 r potential so neglecting the long range electrostatic terms can degrade qualitative results especially for highly charged systems There are other fast evaluation methods that approximate the contribution to the long range electrostatic terms that require O N or O N log N computational cost depending on the met
287. psf solvate psf writepdb solvate pdb Delete the combined water protein molecule and load the system that has excess water removed mol delete top mol load psf solvate psf pdb solvate pdb Return the size of the water box return list list xmin ymin zmin list xmax ymax zmax 4 4 List of Commands e topology list lt file name gt Purpose Read in molecular topology definitions from file Arguments lt file name gt CHARMM format topology file list Lists all currently specified topology files residues Return a list of the known residue topologies patches Return a list of the known residue patches Context Beginning of script before segment May call multiple times e topology alias lt alternate residue name gt lt existing residue name gt Purpose Provide alternate names for residues found in topology file An alternate name used to generate a residue will be used on output Compare to pdbalias residue below in which the real name is used on output Arguments lt alternate residue name gt Desired residue name lt existing residue name gt Residue name found in topology file Context Before reading sequence with pdb May call multiple times e pdbalias residue lt alternate name gt lt real name gt Purpose Provide translations from residues found in PDB files to proper residue names read in from topology definition files Proper names from topology files will be used in generated PSF
288. ptTempRescaling lt send temperature to velocity rescaling thermostat gt Acceptable Values on or off Default Value on Description Setting this to on will cause the veloctiy rescaling thermostat to use the updated temperatures from adaptive tempering Note that either one of adaptTempLangevin or adaptTempRescaling have to be on adaptTempOutFreq lt steps between printing adaptive tempering output gt Acceptable Values Positive integers Default Value 10 Description The number of timesteps between printing adaptive tempering output to the log file adaptTempFirstStep lt step to start adaptive tempering gt Acceptable Values Non negative integers Default Value 0 Description The first timestep from which adaptive tempering will be run adaptTempLastStep lt step to stop adaptive tempering gt Acceptable Values Positive integers Description The last timestep to apply adaptive tempering adaptTempCgamma lt dynamic bin averaging constant gt Acceptable Values Non negative real number Default Value 0 1 Description The calculation of the mean energy for a given bin is weighted by a factor of 1 Cgamma samples to damp out old statistics Setting Cgamma to zero restores the use of a standard arithmetic mean to calculate the mean energy for each bin adaptTempRandom lt assign random temperature if we step out of range gt Acceptable Values on or off Default Value off Description If set to on and the
289. ption If both switching and vdwForceSwitching are set to on then CHARMM force switching is used for van der Waals forces LJcorrection as implemented is incon sistent with vdwForceSwitching e switchdist lt distance at which to activate switching splitting function for electrostatic 49 and van der Waals calculations A gt Acceptable Values positive decimal lt cutoff Description Distance at which the switching function should begin to take effect This parameter only has meaning if switching is set to on The value of switchdist must be less than or equal to the value of cutoff since the switching function is only applied on the range from switchdist to cutoff For a complete description of the non bonded force parameters see Section 5 2 exclude lt non bonded exclusion policy to use gt Acceptable Values none 1 2 1 3 1 4 or scaled1 4 Description This parameter specifies which pairs of bonded atoms should be excluded from non bonded interactions With the value of none no bonded pairs of atoms will be excluded With the value of 1 2 all atom pairs that are directly connected via a linear bond will be excluded With the value of 1 3 all 1 2 pairs will be excluded along with all pairs of atoms that are bonded to a common third atom i e if atom A is bonded to atom B and atom B is bonded to atom C then the atom pair A C would be excluded With the value of 1 4 all 1 3 pairs will be excluded along with all pairs conne
290. r 177 accelMDTE parameter 177 adaptTempBins parameter 178 adaptTempCgamma parameter 179 adaptTempDt parameter 178 adaptTempFirstStep parameter 179 adaptTempFreq parameter 178 adaptTempInFile parameter 178 adaptTempLangevin parameter 179 adaptTempLastStep parameter 179 adaptTempMD parameter 178 adaptTempOutFreq parameter 179 adaptTempRandom parameter 179 adaptTempRescaling parameter 179 adaptTempRestartFile parameter 179 adaptTempRestartFreq parameter 179 adaptTempTmax parameter 178 adaptTempTmin parameter 178 alch parameter 168 alchCol parameter 169 alchDecouple parameter 171 alchElecLambdaStart parameter 169 alchEquilSteps parameter 168 alchFile parameter 168 alchLambda parameter 17 168 alchLambda2 parameter 17 168 alchOutFile parameter 169 alchOutFreq parameter 169 alchType parameter 168 alchVdwLambdaEnd parameter 170 alchVdwShift Coeff parameter 169 alias psfgen command 39 44 alphaCutoff parameter 71 219 amber parameter 28 ambercoor parameter 28 analysis colvars global keyword 116 angleRef colvars alpha keyword 142 angleTol colvars alpha keyword 142 applyBias colvars abf keyword 150 atomNameResidueRange colvars atom group keyword 126 atomNumbers colvars atom group keyword 125 atomNumbersRange colvars atom group key word 126 atoms colvars cartesian keyword 134 atoms colvars rmsd keyword 136 Atoms moving too fast 89 atomsCol colvars atom group keyword 126
291. r a PSF file was read by command readpsf Here a a simple axample PSF 1 NTITLE REMARKS original generated structure x plor psf file REMARKS 4 patches were applied to the molecule REMARKS topology 1LOV_autopsf temp top REMARKS segment P1 first NTER last CTER auto angles dihedrals REMARKS segment 01 first NONE last NONE auto none REMARKS segment W1 first NONE last NONE auto none REMARKS defaultpatch NTER P1 1 REMARKS defaultpatch CTER P1 104 REMARKS patch DISU P1 10 P1 2 REMARKS patch DISU P1 103 P1 6 1704 NATOM 1 P1 1 ALA N NH3 0 300000 14 0070 0 All patches that were applied explicitely using the patch command are listed following the keyword patch but the patches that result from default patching like the first and last patches of a segment are marked as defaultpatch Further the segment based patching rules are listed along with the angle dihedral autogeneration rules 45 5 Force Field Parameters 5 1 Potential energy functions Evaluating the force is the most computationally demanding part of molecular dynamics The force is the negative gradient of a scalar potential energy function F VUC 1 and for systems of biomolecules this potential function involves the summing U r y Ubonded F y Unonbonded 7 2 over a large number of bonded and nonbonded terms The bonded potential terms involve 2 3 and 4 body interactions of covalently bonded atoms
292. r non CUDA binaries module load cudatoolkit For CUDA or large simulations on XE XK use gemini_gni crayxe persistent smp and for smaller XE simulations use gemini_gni crayxe persistent For XC similarly use gni crayxc persistent smp or gni crayxc persistent For XE XK use CRAY XE gnu and for CUDA the with cuda config option the appropri ate charm arch parameter and with fftw3 For XC use instead CRAY XC intel but all other options the same Your batch job will need to load modules and set environment variables module swap PrgEnv cray PrgEnv gnu module load rca module load craype hugepages8M setenv HUGETLB_DEFAULT_PAGE_SIZE 8M setenv HUGETLB_MORECORE no To run an SMP build with one process per node on 16 32 core nodes aprun n 16 r 1 N 1 d 31 path to namd2 ppn 30 pemap 1 30 commap O lt configfile gt or the same with 4 processes per node aprun n 64 N 4 d 8 path to namd2 ppn 7 pemap 1 7 9 15 17 23 25 31 commap 0 8 16 24 lt configfile gt or non SMP leaving one core free for the operating system aprun n 496 r 1 N 31 d 1 path to namd2 pemap 0 30 lt configfile gt The explicit pemap and commap settings are necessary to avoid having multiple threads assigned to the same core or potentially all threads assigned to the same core If the performance of NAMD running on a single compute node is much worse than comparable non Cray host then 1t is very likely that your CPU affinity setti
293. r than minimum image distance gt Context distanceZ distanceXY Acceptable Values boolean Default Value no 132 Description This parameter has the same meaning as that described above for the distance component e oneSiteSystemForce lt Measure system force on group main only gt Context distanceZ distanceXY Acceptable Values boolean Default Value no Description If this is set to yes the system force is measured along a vector field see equation 53 in section 10 5 1 that only involves atoms of main This option is only useful for ABF or custom biases that compute system forces See section 10 5 1 for details This component returns a number in A whose range is determined by the chosen boundary conditions For instance if the z axis is used in a simulation with periodic boundaries the returned value ranges between b 2 and b 2 where b is the box length along z this behavior is disabled if forceNoPEC is set distanceXY modulus of the projection of a distance vector on a plane The distanceXY block defines a distance projected on a plane and accepts the same keywords as the component distanceZ i e main ref either ref2 or axis and oneSiteSystemForce It returns the norm of the projection of the distance vector between main and ref onto the plane orthogonal to the axis The axis is defined using the axis parameter or as the vector joining ref and ref2 see distanceZ above distanceVec distance vect
294. r than the geometric colvar itself The physical unit for this force is kcal mol divided by the colvar unit 10 2 4 Extended Lagrangian The following options enable extended system dynamics where a colvar is coupled to an additional degree of freedom fictitious particle by a harmonic spring All biasing and confining forces are then applied to the extended degree of freedom The actual geometric colvar function of Cartesian coordinates only feels the force from the harmonic spring and its wall potentials if any e extendedLagrangian lt Add extended degree of freedom gt Context colvar Acceptable Values boolean Default Value off Description Adds a fictitious particle to be coupled to the colvar by a harmonic spring The fictitious mass and the force constant of the coupling potential are derived from the parameters extendedTimeConstant and extendedFluctuation described below Biasing forces on the colvar are applied to this fictitious particle rather than to the atoms directly This implements the extended Lagrangian formalism used in some metadynamics simula tions 37 The energy associated with the extended degree of freedom is reported under the MISC title in NAMD s energy output e extendedFluctuation lt Standard deviation between the colvar and the fictitious particle colvar unit gt Context colvar Acceptable Values positive decimal Description Defines the spring stiffness for the extendedLagrangian mode by
295. ration radius of gyration of a group of atoms inertia moment of inertia of a group of atoms inertiaZ moment of inertia of a group of atoms around a chosen axis alpha a helix content of a protein segment dihedralPC projection of protein backbone dihedrals onto a dihedral principal component Some components do not return scalar but vector values They can only be combined with vector values of the same type except within a scripted collective variable distanceVec distance vector between two groups distanceDir unit vector parallel to distanceVec cartesian vector of atomic Cartesian coordinates orientation best fit rotation expressed as a unit quaternion In the following all the available component types are listed along with their physical units and the limiting values if any Such limiting values can be used to define lowerBoundary and upperBoundary in the parent colvar 10 4 1 List of available colvar components distance center of mass distance between two groups Thedistance block defines a distance component between two atom groups group1 and group2 group1 lt First group of atoms gt Context distance Acceptable Values Block group1 Description First group of atoms group2 lt Second group of atoms gt Context distance Acceptable Values Block group2 Description Second group of atoms forceNoPBC lt Calculate absolute rather than minimum image distance gt Context d
296. re complicated configuration The system is periodic a coordinate trajectory file and a set of restart files are produced protocol params numsteps 1000 initial config coordinates alanin pdb temperature 300K seed 12345 periodic cell cellBasisVector1l 33 00 0 cellBasisVector2 0 32 0 0 cellBasisVector3 0 0 32 5 output params outputname tmp alanin binaryoutput no DcDfreq 10 restartfreq 100 integrator par timestep force field pa structure parameters exclude 1 4scaling switching switchdist cutoff pairlistdist stepspercycle ams 1 0 rams alanin psf alanin params scaled1 4 1 0 on 8 0 12 0 13 5 20 199 This file shows another simple configuration file for alanin but this time with full electrostatics using PME and multiple timestepping protocol params numsteps initial config 1000 coordinates alanin pdb temperature 300K seed 12345 periodic cell cellBasisVector1l 33 00 0 cellBasisVector2 0 32 0 0 cellBasisVector3 0 0 32 5 output params outputname tmp alanin binaryoutput no DcDfreq 10 restartfreq 100 integrator params timestep 1 0 fullElectFrequency 4 force field params structure alanin psf parameters alanin params exclude scaled1 4 1 4scaling 1 0 switching on switchdist 8 0 cutoff 12 0 pairlistdist 13 5 stepspercycle 20 full electrostatics PME on PMEGridSizeX 32 PMEGridSizeY 32 PMEGridSizeZ 32 200 This file demonstrates t
297. ristophe Chipot Nancy Universit Universit Henri Poincar France Floris Buelens Institute of Structural and Molecular Biology University of London Birkbeck UK and Christopher Harrison University of Illinois Urbana IL USA 165 A al al Na NS e o Ce H KA E Figure 7 Dual topology description for an alchemical simulation Case example of the mutation of alanine into serine The lighter color denotes the non interacting alternate state and the glycine side chains participate in nonbonded interactions with the rest of the protein scaled on the basis of the current value of A It should be clearly understood that these side chains never interact with each other It is noteworthy that end points of alchemical transformations carried out in the framework of the dual topology paradigm have been shown to be conducive to numerical instabilities from molec ular dynamics simulations often coined as end point catastrophes These scenarios are prone to occur when A becomes close to 0 or 1 and incoming atoms instantly appear where other parti cles are already present which results in a virtually infinite potential as the interatomic distance tends towards 0 Such end point catastrophes can be profitably circumvented by introducing a so called soft core potential 7 47 aimed at a gradual scaling of the short range nonbonded interactions of incoming atoms with their environment as shown in Equation 58 What
298. rom topology definition files Proper names from topology files will be used in generated PSF and PDB files This command also exists under the deprecated name alias Arguments lt residue name gt Proper or aliased residue name lt alternate name gt Atom name found in PDB file lt real name gt Atom name found in topology file Context Before reading coordinates with coordpdb May call multiple times coord lt segid gt lt resid gt lt atomname gt lt z y z gt Purpose Set coordinates for a single atom Arguments lt segid gt Segment ID of target atom lt resid gt Residue ID of target atom lt atomname gt Name of target atom lt x y z gt Coordinates to be assigned Context After structure has been generated coordpdb lt file name gt segid mamdbin namdbin file name Purpose Read coordinates from PDB file matching segment residue and atom names Arguments lt file name gt PDB file containing known or aliased residues and atoms lt segid gt If specified override segment IDs in PDB file namdbin Read coordinates from NAMD binary file lt namdbin file name gt NAMD binary file with atoms in same order as PDB file Context After segment has been generated and atom aliases defined guesscoord Purpose Guesses coordinates of atoms for which they were not explicitly set Calculation is based on internal coordinate hints contained in toplogy definition files When these are insufficient wild gu
299. rrectly Calling multiply on connected sets of atoms multiple times will produce unpredictable results as may running other commands after multiply The enhanced atoms are duplicated exactly in the structure they have the same segment residue and atom names They are distinguished only by the value of the B beta column in the pdb file which is O for normal atoms and varies from 1 to the number of copies created for enhanced atoms The enhanced atoms may be easily observed in VMD with the atom selection beta 0 12 3 2 Simulation In practice LES is a simple method used to increase sampling no special output is generated The following parameters are used to enable LES e les lt is locally enhanced sampling active gt Acceptable Values on or off Default Value off Description Specifies whether or not LES is active lesFactor lt number of LES images to use gt Acceptable Values positive integer equal to the number of images present Description This should be equal to the factor used in multiply when creating the structure The interaction potentials for images is divided by lesFactor e lesReduceTemp lt reduce enhanced atom temperature gt Acceptable Values on or off Default Value off Description Enhanced atoms experience interaction potentials divided by lesFactor This allows them to enter regions that would not normally be thermally accessible If this is not desired then the temperature of these atoms may b
300. rrelation function gt Context colvar Acceptable Values velocity coordinate or coordinate p2 Default Value velocity Description With coordinate or velocity the correlation function Cj t II amp to to t is calculated between the variables and or their velocities II amp is the scalar product when calculated between scalar or vector values whereas for quater nions it is the cosine between the two corresponding rotation axes With coordinate_p2 the second order Legendre polynomial 3 cos 1 2 is used instead of the cosine e corrFuncNormalize lt Normalize the time correlation function gt Context colvar Acceptable Values boolean 123 Default Value on Description If enabled the value of the correlation function at t 0 is normalized to 1 otherwise it equals to O amp amp corrFuncLength lt Length of the time correlation function gt Context colvar Acceptable Values positive integer Default Value 1000 Description Length in number of points of the time correlation function corrFuncStride lt Stride of the time correlation function gt Context colvar Acceptable Values positive integer Default Value 1 Description Number of steps between two values of the time correlation function corrFuncOffset lt Offset of the time correlation function gt Context colvar Acceptable Values positive integer Default Value 0 Description The starting
301. rs configuration file In case of a restart the values of parameters such as targetCenters targetNumSteps etc should not be changed manually Moving restraints umbrella sampling The centers of the harmonic restraints can also be changed in discrete stages in this cases a one dimensional umbrella sampling simulation is per formed The sampling windows in simulation are calculated in sequence The colvars trajectory file may then be used both to evaluate the correlation times between consecutive windows and to cal culate the frequency distribution of the colvar of interest in each window Furthermore frequency distributions on a predefined grid can be automatically obtained by using the histogram bias see 10 5 6 To activate an umbrella sampling simulation the same keywords as in the previous section can be used with the addition of the following e targetNumStages lt Number of stages for steering gt Context harmonic Acceptable Values non negative integer Default Value 0 Description If non zero sets the number of stages in which the restraint centers or force constant are changed to their target values If zero the change is continuous Each stage lasts targetNumSteps MD steps To sample both ends of the transformation the simulation should be run for targetNumSteps x targetNumStages 1 Changing force constant The force constant of the harmonic restraint may also be changed to equilibrate 22 159 e targetForceCons
302. ructure For each set of coordinates x1 t xo t xw t the colvar component rmsd calculates the optimal rotation U ba that best superimposes the coordinates x t onto a set of reference coordinates xh Both the current and the reference coordinates are centered on their centers of geometry Xcog t and x ee The root mean square displacement is then defined as N RMSD xi 4 4 JU Gilt xeos EL i 1 The optimal rotation U Gi Oe is calculated within the formalism developed in reference 19 J ref A which guarantees a continuous dependence of UPu 0i tx with respect to x t The options for rmsd are e atoms lt Atom group gt Context rmsd Acceptable Values atoms block Description Defines the group of atoms of which the RMSD should be calculated Optimal fit options such as refPositions and rotateReference should typically NOT be set within this block Exceptions to this rule are the special cases discussed in the Advanced usage paragraph below e refPositions lt Reference coordinates gt Context rmsd Acceptable Values space separated list of x y z triplets Description This option mutually exclusive with refPositionsFile sets the reference coordinates If only centerReference is on the list can be a single x y z triplet if also rotateReference is on the list should be as long as the atom group This option is independent from that with the same keyword within th
303. s Arguments lt factor gt lt segid resid atomname gt segment residue or atom to be multiplied If resid is omitted the 41 entire segment is multiplied if atomname is omitted the entire residue is multiplied May be repeated as many times as necessary to include all atoms Context After one or more segments have been built all patches applied and coordinates guessed The effects of this command may confuse other commands delatom lt segid gt resid atom name Purpose Delete one or more atoms If only segid is specified all atoms from that segment will be removed from the structure If both segid and resid are specified all atoms from just that residue will be removed If segid resid and atom name are all specified just a single atom will be removed Arguments lt segid gt Name of segment lt resid gt Name of residue optional lt atom name gt Name of atom optional Context After all segments have been built and patched resetpsf Purpose Delete all segments in the structure The topology definitions and aliases are left intact If you want to clear the topology and aliases as well use psfcontext reset instead Arguments Context After one or more segments have been built psfcontext context new delete Purpose Switches between complete contexts including structure topology definitions and aliases If no arguments are provided the current context is returned If lt context gt or new
304. s The file readers in NAMD and VMD can detect and adapt to the endianness of the machine on which the binary file was written and the utility program flipbinpdb is also provided to reformat these files if needed Positions in NAMD binary files are stored in A Velocities in NAMD binary files are stored in NAMD internal units and must be multiplied by PDBVELFACTOR 20 45482706 to convert to A ps Forces in NAMD binary files are stored in kcal mol A 3 2 NAMD configuration parameters 3 2 1 Input files e coordinates lt coordinate PDB file gt Acceptable Values UNIX filename Description The PDB file containing initial position coordinate data Note that path names can be either absolute or relative Only one value may be specified e structure lt PSF file gt Acceptable Values UNIX filename Description The X PLOR format PSF file describing the molecular system to be simu lated Only one value may be specified e parameters lt parameter file gt Acceptable Values UNIX filename Description A CHARMM19 CHARMM22 or CHARMM27 parameter file that defines all or part of the parameters necessary for the molecular system to be simulated At least one parameter file must be specified for each simulation Multiple definitions but only one file per definition are allowed for systems that require more than one parameter file The files will be read in the order that they appear in the configuration file If duplicate parameters are read a w
305. s but the binary files are not guaranteed to be transportable between computer architectures The atom count record is used to detect wrong endian files which works for most atom counts The utility program flipbinpdb is provided to reformat these files if necessary DCDfile lt coordinate trajectory output file gt Acceptable Values UNIX filename Default Value outputname dcd Description The binary DCD position coordinate trajectory filename This file stores the trajectory of all atom position coordinates using the same format binary DCD as X PLOR If DCDfile is defined then DCDfreq must also be defined 25 DCDfreq lt timesteps between writing coordinates to trajectory file gt Acceptable Values positive integer Description The number of timesteps between the writing of position coordinates to the trajectory file The initial positions will not be included in the trajectory file Positions in DCD files are stored in A DCDUnitCell lt write unit cell data to dcd file gt Acceptable Values yes or no Default Value yes if periodic cell Description If this option is set to yes then DCD files will contain unit cell information in the style of Charmm DCD files By default this option is enabled if the simulation cell is periodic in all three dimensions and disabled otherwise velDCDfile lt velocity trajectory output file gt Acceptable Values UNIX filename Default Value outputname veldcd Description The bi
306. s positive decimal Description Initial temperature value for the system Using this option will generate a random velocity distribution for the initial velocities for all the atoms such that the system is at the desired temperature Either the temperature or the velocities binvelocities option must be defined to determine an initial set of velocities Both options cannot be used together e COMmotion lt allow initial center of mass motion gt Acceptable Values yes or no Default Value no Description Specifies whether or not motion of the center of mass of the entire system is allowed If this option is set to no the initial velocities of the system will be adjusted to remove center of mass motion of the system Note that this does not preclude later center of mass motion due to external forces such as random noise in Langevin dynamics boundary potentials and harmonic restraints e seed lt random number seed gt Acceptable Values positive integer Default Value pseudo random value based on current UNIX clock time Description Number used to seed the random number generator if temperature or langevin is selected This can be used so that consecutive simulations produce the same results If no value is specified NAMD will choose a pseudo random value based on the current UNIX clock time The random number seed will be output during the simulation startup so that its value is known and can be reused for subsequent simulations Note t
307. s positive decimal Description Temperature to which atoms affected by Langevin dynamics will be adjusted This temperature will be roughly maintained across the affected atoms through the addition of friction and random forces e langevinDamping lt damping coefficient for Langevin dynamics 1 ps gt Acceptable Values positive decimal Default Value per atom values from PDB file Description Langevin coupling coefficient to be applied to all atoms unless langevinHydrogen is off in which case only non hydrogen atoms are affected If not given a PDB file is used to obtain coefficients for each atom see langevinFile and langevinCol below e langevinHydrogen lt Apply Langevin dynamics to hydrogen atoms gt Acceptable Values on or off Default Value on Description If langevinDamping is set then setting langevinHydrogen to off will turn off Langevin dynamics for hydrogen atoms This parameter has no effect if Langevin coupling coefficients are read from a PDB file e langevinFile lt PDB file containing Langevin parameters gt Acceptable Values UNIX filename Default Value coordinates 80 Description PDB file to use for the Langevin coupling coefficients for each atom If this parameter is not specified then the PDB file specified by coordinates is used e langevinCol lt column of PDB from which to read coefficients gt Acceptable Values X Y Z 0 or B Default Value 0 Description Column of the PDB file to use for th
308. s a 3 D vector in the form of a Tcl list e dihedralgrad lt coor1 gt lt coor2 gt lt coor3 gt lt coor4 gt A dihedral defined by four atoms is a function of their coordinates ri r2 r3 74 in radian This command takes the coordinates of the four atoms as input and returns a list of Je oe oe Each element of the list is a 3 D vector in the form of a Tcl list 2 r3 T4 107 As an example here s a script which applies a harmonic constraint reference position being 0 to a dihedral Note that the addenergy line is not really necessary it simply adds the calculated constraining energy to the MISC column which is displayed in the energy output tclForcesScript 41 The IDs of the four atoms defining the dihedral set aidi 112 set aid2 123 set aid3 117 set aid4 115 The spring constant for the harmonic constraint set k 3 0 addatom aid1 addatom aid2 addatom aid3 addatom aid4 set PI 3 1416 proc calcforces global aidi aid2 aid3 aid4 k PI loadcoords p Calculate the current dihedral set phi getdihedral p aid1 p aid2 p aid3 p aid4 Change to radian set phi expr phi PI 180 optional Add this constraining energy to MISC in the energy output addenergy expr k phi phi 2 0 Calculate the force along the dihedral according to the harmonic constraint set force expr k phi Calculate the gradients foreach g1 g2 g3 g4 dihedralgrad p aid1 p aid2 p a
309. s a final target structure by means of steering forces At each timestep the RMS distance between the current coordinates and the target structure is computed after first aligning the target structure to the current coordinates The force on each atom is given by the gradient of the potential Urmp gt RMS t RMS t 31 where RMS t is the instantaneous best fit RMS distance of the current coordinates from the target coordinates and RM S t evolves linearly from the initial RMSD at the first TMD step to the final RMSD at the last TMD step The spring constant k is scaled down by the number N of targeted atoms Atoms can be separated into non overlapping constraint domains by assigning integer values in the beta column of the TMDFile Forces on the atoms will be calculated for each domain independently of the other domains Within each domain the set of atoms used to fit the target structure can be different from the set of atoms that are biased towards the target structure If the altloc field in the TMDFile is not or 0 then the atom is fitted If the occupancy is non zero then the atom is biased If none of the atoms in a domain have altloc set then all biased atoms are fitted Note that using different atoms for fitting and biasing or not using the same spring constant for all target atoms within a domain will result in forces conserving neither energy nor momentum In this case harmonic restraints and Langevin dynami
310. s added to the MISC output field The replace flag should be 1 if the external program force should replace the forces calculated by NAMD for that atom and 0 if the forces should be added For best performance the file should be in tmp and not on a network mounted filesystem 112 10 Collective Variable based Calculations In today s molecular dynamics simulations it is often useful to reduce the large number of degrees of freedom of a physical system into few parameters whose statistical distributions can be analyzed individually or used to define biasing potentials to alter the dynamics of the system in a controlled manner These have been called order parameters collective variables surrogate reaction coordinates and many other terms Here we use primarily the term collective variable shortened to colvar which indicates any differentiable function of atomic Cartesian coordinates 2 with i between 1 and N the total number of atoms E Elet a erlt 1 lt i j k lt N 35 The colvars module in NAMD may be used in both MD simulations and energy minimization runs The module is designed to perform multiple tasks concurrently during or after a simulation the most common of which are e apply restraints or biasing potentials to multiple colvars tailored on the system by choosing from a wide set of basis functions without limitations on their number or on the number of atoms involved while this can in pri
311. s between 1 alchVdwLambdaEnd and 1 0 VdW interactions are only fully decoupled when A reaches 1 0 e alchDecouple lt Disable scaling of nonbonded interactions within alchemical partitions gt Acceptable Values on or off Default Value off Description With alchDecouple set to on only nonbonded interactions of perturbed incoming and outgoing atoms with their environment are scaled while interactions within the subset of perturbed atoms are preserved On the contrary if alchDecouple is set to off interactions within the perturbed subset of atoms are also scaled and contribute to the cumulative free energy In most calculations intramolecular annihilation free energies are not particularly informative and decoupling ought to be preferred Under certain circumstances it may however be desirable to scale intramolecular interactions provided that the latter are appropriately accounted for in the thermodynamic cycle 17 11 3 Examples of input files for running alchemical free energy calculations The first example illustrates the use of TCL scripting for running an alchemical transformation with the FEP feature of NAMD In this calculation A is changed continuously from 0 to 1 by increments of A 0 1 alch On Enable alchemical simulation module alchType fep Set alchemical method to FEP alchFile ion fep File containing the information about grow alchCol X ing shrinking atoms described in column X alchOutfile ion fepout Output fil
312. s of the long range electrostatic forces which contribute to resonance along bonds to hydrogen atoms allowing a fullElectFrequency of 6 vs 4 with a 1 fs timestep without using rigidBonds all You may use rigidBonds water but using rigidBonds all with MOLLY makes no sense since the degrees of freedom which MOLLY protects from resonance are already frozen 79 e mollyTolerance lt allowable error for MOLLY gt Acceptable Values positive decimal Default Value 0 00001 Description Convergence criterion for MOLLY algorithm e mollyIterations lt maximum MOLLY iterations gt Acceptable Values positive integer Default Value 100 Description Maximum number of iterations for MOLLY algorithm 7 4 Temperature Control and Equilibration 7 4 1 Langevin dynamics parameters NAMD is capable of performing Langevin dynamics where additional damping and random forces are introduced to the system This capability is based on that implemented in X PLOR which is detailed in the X PLOR User s Manual 13 although a different integrator is used e langevin lt use Langevin dynamics gt Acceptable Values on or off Default Value off Description Specifies whether or not Langevin dynamics active If set to on then the parameter langevinTemp must be set and the parameters langevinFile and langevinCol can optionally be set to control the behavior of this feature e langevinTemp lt temperature for Langevin calculations K gt Acceptable Value
313. s or away from a target structure respectively Forces are applied only if RM S t is betwween TMDInitialRMSD and RMS x t in other words only if the current RMSD fails to keep pace with the target value TMDDiffRMSD lt Is double sided TMD active gt Acceptable Values on or off Default Value off Description Turns on the double sided TMD feature which targets the transition between two structures This is accomplished by modifying the TMD force such that the potential is based on the difference of RMSD s from the two structures a DRMS t DRMS t 32 102 where DRM S t is RMS1 t RMS2 2 RMS1 being the RMSD from structure 1 and RMS2 the RMSD from structure 2 The first structure is specified as normal in TMDFile and the second structure should be specified in TMDFile2 preserving any domain designations found in TMDFile e TMDFile2 lt Second structure file for double sided TMD gt Acceptable Values Path to PDB file Description PDB file defining the second structure of a double sided TMD This file should contain the same number of atoms as TMDFile along with the same domain designations if any are specified 9 8 Steered Molecular Dynamics SMD The SMD feature is independent from the harmonic constraints although it follows the same ideas In both SMD and harmonic constraints one specifies a PDB file which indicates which atoms are tagged as constrained The PDB file also gives initial coordinates for
314. s to create a complete molecular building solution We welcome your feedback on this new tool 4 1 Ordinary Usage psfgen is currently distributed in two forms One form is as a standalone program implemented as a Tcl interpreter which reads commands from standard output You may use loops variables etc as you would in a VMD or NAMD script You may use psfgen interactively but we expect it to be run most often with a script file redirected to standard input The second form is as a Tcl package which can be imported into any Tcl application including VMD All the commands available to the standalone version of psfgen are available to the Tcl package using psfgen within VMD lets you harness VMD s powerful atom selection capability as well as instantly view the result of your structure building scripts Examples of using psfgen both with and without VMD are provided in this document Generating PSF and PDB files for use with NAMD will typically consist of the following steps 1 Preparing separate PDB files containing individual segments of protein solvent etc before running psfgen 2 Reading in the appropriate topology definition files and aliasing residue and atom names found in the PDB file to those found in the topology files This will generally include selecting a default protonation state for histidine residues 3 Generating the default structure using segment and pdb commands 4 Applying additional patches to the structure 5
315. scription Defines the lowest end of the interval of relevant values for the colvar This number can be either a true physical boundary or a user defined number Together with upperBoundary and width it is used to define a grid of values along the colvar not available for colvars based on distanceDir distanceVec and orientation This option does not affect dynamics to confine a colvar within a certain interval the options lowerWall and lowerWallConstant should be used e upperBoundary lt Upper boundary of the colvar gt Context colvar Acceptable Values decimal Description Similarly to lowerBoundary defines the highest possible or allowed value e hardLowerBoundary lt Whether the lower boundary is the physical lower limit gt Context colvar Acceptable Values boolean Default Value off 119 Description This option does not affect simulation results but enables some internal opti mizations Depending on its mathematical definition a colvar may have natural boundaries for example a distance colvar has a natural lower boundary at 0 Setting this option in structs the colvars module that the user defined lower boundary is natural See Section 10 4 for the physical ranges of values of each component e hardUpperBoundary lt Whether the upper boundary is the physical upper limit of the colvar s values gt Context colvar Acceptable Values boolean Default Value off Description Analogous to hard
316. scription of the Adaptive Biasing Force method see reference 20 For details about this implementation see references 34 and 35 When publishing research that makes use of this functionality please cite references 20 and 35 An alternate usage of this feature is the application of custom tabulated biasing potentials to one or more colvars See inputPrefix and updateBias below ABF is based on the thermodynamic integration TI scheme for computing free energy profiles The free energy as a function of a set of collective variables iep1 n is defined from the canonical distribution of P amp AE gt In P E Ao 49 In the TI formalism the free energy is obtained from its gradient which is generally calculated in the form of the average of a force F exerted on taken over an iso surface VEA E Fog 50 Several formulae that take the form of 50 have been proposed This implementation relies partly on the classic formulation 15 and partly on a more versatile scheme originating in a work by Ruiz Montero et al 61 generalized by den Otter 21 and extended to multiple variables by Ciccotti et al 18 Consider a system subject to constraints of the form o x 0 Let V ie 1 n be arbitrarily chosen vector fields R RIN verifying for all i j and k Vi Va Es ds 51 Vi Ve Ok 0 52 then the following holds 18 oA DE vi a Vz V kel Vz vijg 53 where V
317. se PME because it is not compatible with GBIS Periodic boundary conditions are supported but are optional User s will need to increase cutoff 16 18 A is a good place to start but user s will have to check their system s behavior and increase cutoff accordingly GBIS interactions are never excluded regardless of the type of force field used thus user s can choose any value for exclude without affecting GBIS user s should still choose exclude based on the force field as if using explicit solvent When using GBIS multiple timestepping behaves as follows the dEdr force is calculated every nonbondedFreq steps as with explicit solvent 2 is a reasonable frequency and the dEda force is calculated every fullElectFrequency steps because dEda varies more slowly than dEdr 4 is a reasonable frequency GBIS lt Use Generalized Born Implicit Solvent gt Acceptable Values on or off Default Value off Description Turns on GBIS method in NAMD solventDielectric lt dielectric of water gt Acceptable Values positive decimal Default Value 78 5 Description Defines the dielectric of the solvent usually 78 5 or 80 intrinsicRadiusOffset lt shrink the intrinsic radius of atoms A gt Acceptable Values positive decimal Default Value 0 09 Description This offset shrinks the intrinsic radius of atoms used only for calculating Born radius to give better agreement with Poisson Boltzmann calculations Most users should not change this
318. setting the typical deviation between the colvar and the extended degree of freedom due to thermal fluctuation The spring force constant is calculated internally as kgT 0 where is the value of extendedFluctuation e extendedTimeConstant lt Oscillation period of the fictitious particle fs gt Context colvar Acceptable Values positive decimal Default Value 200 Description Defines the inertial mass of the fictitious particle by setting the oscillation period of the harmonic oscillator formed by the fictitious particle and the spring The period should be much larger than the MD time step to ensure accurate integration of the extended particle s equation of motion The fictitious mass is calculated internally as kgT t 270 where 7 is the period and is the typical fluctuation see above e extendedTemp lt Temperature for the extended degree of freedom K gt Context colvar Acceptable Values positive decimal Default Value thermostat temperature 122 Description Temperature used for calculating the coupling force constant of the extended coordinate see extendedFluctuation and if needed as a target temperature for extended Langevin dynamics see extendedLangevinDamping This should normally be left at its default value e extendedLangevinDamping lt Damping factor for extended Langevin dynamics ps gt Context colvar Acceptable Values positive decimal Default Value 1 0 Description If this is non zero
319. sin d2 cos dy sin dy Note that angles and Yy have little impact on chain conformation and are therefore discarded following the implementation of dPCA in the analysis software Carma 27 For a given principal component eigenvector of coefficients k 1 lt i lt s m 1 the projection of the current backbone conformation is N 1 E y Kan 3 COS Wn kan 2 Sin Wn kan 1 cos Pn 1 kan sinl n 1 47 n 1 dihedralPC expects the same parameters as the alpha component for defining the relevant residues residueRange and psfSegID in addition to the following e vectorFile lt File containing dihedral PCA eigenvector s gt Context dihedralPC Acceptable Values file name Description A text file containing the coefficients of dihedral PCA eigenvectors on the cosine and sine coordinates The vectors should be arranged in columns as in the files output by Carma 27 e vectorNumber lt File containing dihedralPCA eigenvector s gt Context dihedralPC Acceptable Values positive integer Description Number of the eigenvector to be used for this component 10 4 2 Advanced usage and special considerations Periodic components The following components returns real numbers that lie in a periodic interval e dihedral torsional angle between four groups e spinAngle angle of rotation around a predefined axis in the best fit from a set of reference coordinates In certain conditions distanceZ can also be periodic name
320. sing an MPI library that takes advantage of special networking hardware Directions for compiling NAMD are contained in the release notes which are available from the NAMD web site http www ks uiuc edu Research namd and are included in all distributions 18 5 Documentation All available NAMD documentation is available for download without registration via the NAMD web site http www ks uiuc edu Research namd 212 References 1 11 12 13 14 15 16 M P Allen and D J Tildesley Computer Simulation of Liquids Oxford University Press New York 1987 A Altis P H Nguyen R Hegger and G Stock Dihedral angle principal component analysis of molecular dynamics simulations J Chem Phys 126 24 244111 2007 P H Axelsen and D Li Improved convergence in dual topology free energy calculations through use of harmonic restraints J Comput Chem 19 1278 1283 1998 A Barducci G Bussi and M Parrinello Well tempered metadynamics A smoothly converg ing and tunable free energy method Phys Rev Lett 100 020603 2008 C H Bennett Efficient estimation of free energy differences with monte carlo data J Comp Phys 22 245 268 1976 F C Bernstein T F Koetzle G J B Williams J E F Meyer M D Brice J R Rodgers O Kennard T Shimanouchi and M Tasumi The protein data bank A computer based archival file for macromolecular structures J Mol Biol 112 5
321. sname gt Residue type name from topology file lt chain gt Single character chain identi fier Context Anywhere within segment 40 e pdb lt file name gt Purpose Extract sequence information from PDB file when building segment Residue IDs will be preserved residue names must match entries in the topology file or should be aliased before pdb is called Arguments lt file name gt PDB file containing known or aliased residues Context Anywhere within segment e mutate lt resid gt lt resname gt Purpose Change the type of a single residue in the current segment Arguments lt resid gt Unique name for residue 1 5 characters usually numeric lt resname gt New residue type name from topology file Context Within segment after target residue has been created e patch list lt patch residue name gt lt segid resid gt Purpose Apply a patch to one or more residues Patches make small modifications to the structure of residues such as converting one to a terminus changing the protonation state or creating disulphide bonds between a pair of residues Arguments list Lists all patches applied explicitey using the command patch listall Lists all currently applied patches including default patches lt patch residue name gt Name of patch residue from topology definition file lt segid resid gt List of segment and residue pairs to which patch should be applied Context After one or more segments have been
322. ssing and analysis Other output files may be written by specific methods applied to the colvars e g by the ABF method see 10 5 1 or the metadynamics method see 10 5 2 Like the colvar trajectory file they are needed only for analyzing not continuing a simulation All such files names also begin with the prefix outputName Finally the total energy of all biases or restraints applied to the colvars appears under the NAMD standard output under the MISC column 10 2 Defining collective variables and their properties In the configuration file each colvar is defined by the keyword colvar followed by its configura tion options within curly braces colvar One of these options is the name of a colvar component for example including rmsd defines the colvar as a RMSD function In most applications only one component is used and the component is equal to the colvar The full list of colvar components can be found in Section 10 4 with the syntax to select atoms in Section 10 3 The following section lists several options to control the behavior of a single colvar regardless of its type 118 10 2 1 General options for a collective variable The following options are not required by default however the first four are very frequently used e name lt Name of this colvar gt Context colvar Acceptable Values string Default Value colvar numeric id Description The name is an unique case sensitive string which
323. ssure profile gt Acceptable Values on or off Default Value off Description When active NAMD will compute kinetic bonded and nonbonded but not reciprocal space contributions to the pressure profile Results will be recorded in the NAMD output file in lines with the format PRESSUREPROFILE ts Axx Ayy Azz Bxx Byy Bzz where ts is the timestep followed by the three diagonal components of the pressure tensor in the first slab the slab with lowest z then the next lowest slab and so forth The output will reflect the pressure profile averaged over all the steps since the last output NAMD also reports kinetic bonded and nonbonded contributions separately using the same format as the total pressure but on lines beginning with PPROFILEINTERNAL PPROFILEBONDED and PPROFILENONBONDED e pressureProfileSlabs lt Number of slabs in the spatial partition gt Acceptable Values Positive integer Default Value 10 192 Description NAMD divides the entire periodic cell into horizontal slabs of equal thickness pressureProfileSlabs specifies the number of such slabs pressureProfileFreq lt How often to output pressure profile data gt Acceptable Values Positive integer Default Value 1 Description Specifies the number of timesteps between output of pressure profile data pressureProfileEwald lt Enable pressure profile Ewald sums gt Acceptable Values on or off Default Value off Description When enabled only the Ewa
324. st mode gt Acceptable Values on or off Default Value off Description When accelMDdual is on aMD switches to the dual boost mode Two inde pendent boost potentials will be applied one to the dihedral potential that is controlled by 176 the parameters accelMDE and accelMDalpha and a second to the Total Dihedral potential that is controlled by the accelMDTE and accelMDTalpha parameters described below accelMDTE lt Threshold energy E in the dual boost mode gt Acceptable Values Real number Description Specifies the threshold energy E used in the calculation of boost energy for the Total Dihedral potential This option is only available when accelMDdual is turned on accelMDTalpha lt Acceleration factor a in the dual boost mode gt Acceptable Values Positive real number Description Specifies the acceleration factor a used in the calculation of boost energy for the Total Dihedral potential This option is only available when accelMDdual is turned on accelMDFirstStep lt First accelerated MD step gt Acceptable Values Zero or positive integer Default Value 0 Description Accelerated MD will only be performed when the current step is equal to or higher than accelMDFirstStep and equal to or lower than accelMDLastStep Otherwise regular MD will be performed accelMDLastStep lt Last accelerated MD step gt Acceptable Values Zero or positive integer Default Value 0 Description Accelerated MD wil
325. stions pushing for new features and testing bug ridden code 14 2 Getting Started 2 1 What is needed Before running NAMD explained in section 17 the following are be needed e A CHARMM force field in either CHARMM or X PLOR format e An X PLOR format PSF file describing the molecular structure e The initial coordinates of the molecular system in the form of a PDB file e A NAMD configuration file NAMD provides the psf gen utility documented in Section 4 which is capable of generating the required PSF and PDB files by merging PDB files and guessing coordinates for missing atoms If psfgen is insufficient for your system we recommend that you obtain access to either CHARMM or X PLOR both of which are capable of generating the required files 2 2 NAMD configuration file Besides these input and output files NAMD also uses a file referred to as the configuration file This file specifies what dynamics options and values that NAMD should use such as the number of timesteps to perform initial temperature etc The options and values in this file control how the system will be simulated The NAMD configuration file is specified on the NAMD command line either before or after the various parallel execution options described in section 17 A NAMD configuration file contains a set of options and values The options and values specified determine the exact behavior of NAMD what features are active or inactive how long the simulation shou
326. straints The linear restraint biasing method is used to minimally bias a simulation There is generally a unique strength of bias for each CV center which means you must know the bias force constant specifically for the center of the CV This force constant may be found by using experiment directed simulation described in section 10 5 5 Please cite Pitera and Chodera when using 58 e forceConstant lt Scaled force constant kcal mol gt Context linear Acceptable Values positive decimal Default Value 1 0 Description This defines a scaled force constant for the linear bias To ensure consis tency for multidimensional restraints it is divided internally by the specific width for each colvar involved which is 1 by default so that all colvars are effectively dimensionless and of commensurate size e centers lt Initial linear restraint centers gt Context linear Acceptable Values space separated list of colvar values Description The centers equilibrium values of the restraint are entered here The number of values must be the number of requested colvars Each value is a decimal number if the corresponding colvar returns a scalar a x y z triplet if it returns a unit vector or a vector and a q0 q1 q2 q3 quadruplet if it returns a rotational quaternion If a colvar has periodicities or symmetries its closest image to the restraint center is considered when calculating the linear potential 10 5 5 Adaptive Lin
327. t Reference structure for Go simulation gt Acceptable Values PDB file Description PDB file contains the reference structure used to define the Go potential The file need not be the same file used to initialize the coordinates of the MD simulation however it must contain the same number of atoms in the same order as given in the structure psf and coordinates coor file Additionally the occupancy fields of the PDB file will be read to determine which chain type an individual atom belongs to and thus which pairwise Go potential to use to calculate forces By default the occupancy value of 0 0 turns off the Go potential for that particular atom e GoMethod lt controls method for storing Go contact information gt Acceptable Values lowmem or matrix Description Specifies whether the Go contacts should be calculated on the fly or stored in a matrix respectively In most cases lowmem will be sufficient However for smaller systems the matrix does offer a slight performance speedup in terms of wall time Variable is only used if GoForcesOn is on The following sections describe the format of the GoParameter file 13 1 4 GoParameter format When running a Go simulation the atoms are partitioned into chains according to the occupancy value given in the GoCoordinates file For every possible pairwise combination between chains a Go potential is defined by the following equations Let aed be the pairwise distance be
328. t Value off Description Turns on alchemical transformation methods in NAMD e alchType lt Which method is to be employed for the alchemical transformation gt Acceptable Values fep or ti Default Value ti Description Turns on Hamiltonian scaling and ensemble averaging for alchemical FEP or TI e alchLambda lt Current value of the coupling parameter gt Acceptable Values positive decimal between 0 0 and 1 0 Description The coupling parameter value determining the progress of the perturbation for FEP or TI e alchLambda2 lt Forward projected value of the coupling parameter gt Acceptable Values positive decimal between 0 0 and 1 0 Description The lambda2 value corresponds to the coupling parameter to be used for sam pling in the next window The free energy difference between alchLambda2 and alchLambda is calculated Through simulations at progressive values of alchLambda and alchLambda2 the total free energy difference may be determined e alchEquilSteps lt Number of equilibration steps in a window prior to data collection gt Acceptable Values positive integer less than numSteps or run Default Value 0 Description In each window alchEquilSteps steps of equilibration can be performed before ensemble averaging is initiated The output also contains the data gathered during equilibration and is meant for analysis of convergence properties of the alchemical free energy calculation e alchFile lt pdb file with perturbati
329. t and the real PMF gradient e t temperature for M C sampling unrelated to the simulation temperature 500 K e m use metadynamics like biased sampling 0 false 1 e h increment for the history dependent bias hill height 0 01 kcal mol e f if non zero this factor is used to scale the increment stepwise in the second half of the M C sampling to refine the free energy estimate 0 5 Using the default values of all parameters should give reasonable results in most cases abf_integrate produces the following output files e lt gradient_file gt pmf computed free energy surface e lt gradient_file gt histo histogram of M C sampling not usable in a straightforward way if the history dependent bias has been applied e lt gradient file gt est estimated gradient of the calculated free energy surface from finite differences e lt gradient_file gt dev deviation between the user provided numerical gradient and the ac tual gradient of the calculated free energy surface The RMS norm of this vector field is used as a convergence criteria and displayed periodically during the integration Note Typically the deviation vector field does not vanish as the integration converges This happens because the numerical estimate of the gradient does not exactly derive from a potential due to numerical approximations used to obtain it finite sampling and discretization on a grid 10 5 2 Metadynamics The metady
330. t features in Charm gt When building NAMD with CUDA support you should use the same Charm you would use for a non CUDA build Do NOT add the cuda option to the Charm build command line The only changes to the build process needed are to add with cuda and possibly cuda prefix to the NAMD config command line 17 11 Xeon Phi Acceleration NAMD supports offloading calculations to Intel Xeon Phi coprocessors This feature is new and should be considered experimental Observed speedups are around a factor of two but parallel scaling is degraded The Xeon Phi coprocessor is supported in NAMD similar to CUDA GPUs Binaries are not provided so you will need to build from source code see Compiling NAMD below specify ing with mic to the config script As with CUDA multicore or ibverbs smp builds are strongly recommended A recent Intel compiler is obviously required to compile for Xeon Phi 17 12 Memory Usage NAMD has traditionally used less than 100MB of memory even for systems of 100 000 atoms With the reintroduction of pairlists in NAMD 2 5 however memory usage for a 100 000 atom system with a 12A cutoff can approach 300MB and will grow with the cube of the cutoff This extra memory is distributed across processors during a parallel run but a single workstation may run out of physical memory with a large system To avoid this NAMD now provides a pairlistMinProcs config file option that specifies the minimum number o
331. t is a subset of the DataExplorer DX file format as shown below Lines at the beginning of the file starting with a symbol are ignored as comments Variables replaced by numbers in an actual file E HH HHH HH HH H OH OH OF xn yn and zn are the number of data points along each dimension xorg yorg and zorg is the origin of the grid in angstroms x 1 3 del y 1 3 del and z 1 3 del are the basis vectors which transform grid indices to coordinates in angstroms x i j k xorg i xidel j yidel k zldel y i j k yorg i x2del j y2del k z2del z i j k zorg i x3del j y3del k z3del Grid data follows with three values per line ordered z fast y mediun and x slow Exactly xn yn zn values should be given Grid data is then terminated with a field object Note Other features of the DX file format are not handled by this code object 1 class gridpositions counts xn yn zn origin xorg yorg zorg delta xidel yidel zidel delta x2del y2del z2del delta x3del y3del z3del object 2 class gridconnections counts xn yn zn object 3 class array type double rank 0 items xn yn zn data follows f1 12 f3 f4 f5 f6 93 object 4 class field component positions value 1 component connections value 2 component data value 3 Each dimension of the grid may be specified as continuous or not If the grid is not continuous in a particular dimension the potential grid is padded with one border s
332. t lines lt number_of_tables gt lt table_spacing A gt lt maximum_distance A gt followed by number_of tables energy tables formatted as TYPE lt interaction type name gt O lt energy kcal mol gt lt force kcal mol A gt lt table_spacing gt lt energy kcal mol gt lt force kcal mol A gt lt 2 table_spacing gt lt energy kcal mol gt lt force kcal mol A gt 56 lt 3 table_spacing gt lt energy kcal mol gt lt force kcal mol A gt lt maximum_distance 3 table_spacing gt lt energy kcal mol gt lt force kcal mol A gt lt maximum_distance 2 table_spacing gt lt energy kcal mol gt lt force kcal mol A gt lt maximum_distance table_spacing gt lt energy kcal mol gt lt force kcal mol A gt The table entry at mazimum_distance will match the energy of the previous entry but have a force of zero The maximum distance must be at least equal to the nonbonded cutoff distance and entries beyond the cutoff distance will be ignored For the above example with a cutoff of 12 A the table file could look like parameters for silicon dioxide 3 0 01 14 0 TYPE SIO O 5 092449e 26 3 055469e 31 0 01 5 092449e 14 3 055469e 17 0 02 7 956951e 12 2 387085e 15 0 03 6 985526e 11 1 397105e 14 13 98 0 000000e 00 0 000000e 00 13 99 0 000000e 00 0 000000e 00 TYPE 00 O 1 832907e 27 1 099744e 32 0 01 1 832907e 15 1 099744e 18 0 02 2 863917e 13 8 591751e 15 0 03 2 514276e 12 5 028551e 14 13 98 0
333. t record is used to detect wrong endian files which works for most atom counts The utility program flipbinpdb is provided to reformat these files if necessary restartname lt restart files prefix gt Acceptable Values UNIX filename prefix Default Value outputname restart Description The prefix to use for restart filenames NAMD produces restart files that store the current positions and velocities of all atoms at some step of the simulation This option specifies the prefix to use for restart files in the same way that outputname specifies a filename prefix for the final positions and velocities If restartname is defined then the parameter restartfreq must also be defined restartfreq lt frequency of restart file generation gt Acceptable Values positive integer Description The number of timesteps between the generation of restart files restartsave lt use timestep in restart filenames gt Acceptable Values yes or no Default Value no Description Appends the current timestep to the restart filename prefix producing a sequence of restart files rather than only the last version written binaryrestart lt use binary restart files gt Acceptable Values yes or no Default Value yes Description Enables the use of binary restart files If this option is not set to no then the restart files will be written in binary rather than PDB format Binary files preserve more accuracy between NAMD restarts than ASCII PDB file
334. t the entire system is set to the desired temperature The following parameters specify how often and to what temperature this reassignment is performed e reassignFreq lt number of timesteps between temperature reassignment gt Acceptable Values positive integer Description The equilibration feature of NAMD is activated by specifying the num ber of timesteps between each temperature reassignment If this value is given then the reassignTemp parameter must also be given to specify the target temperature e reassignTemp lt temperature for equilibration K gt Acceptable Values positive decimal Default Value temperature if set otherwise none Description The temperature to which all velocities will be reassigned every reassignFreq timesteps This parameter is valid only if reassignFreq has been set e reassignIncr lt temperature increment for equilibration K gt Acceptable Values decimal Default Value 0 Description In order to allow simulated annealing or other slow heating cooling protocols reassignIncr will be added to reassignTemp after each reassignment Reassignment is carried out at the first timestep The reassignHold parameter may be set to limit the final temperature This parameter is valid only if reassignFreq has been set e reassignHold lt holding temperature for equilibration K gt Acceptable Values positive decimal Description The final temperature for reassignment when reassignIncr is set reassignTe
335. talforces disabletotalforces Enables disables the loadtotalforces command described below which is disabled by default to avoid unneeded work and communication e loadtotalforces lt varname gt Loads the total forces on each requested atom and group in the previous time step in kcal mol A into a local array The total force also includes external forces Note that the 106 loadforces command returns external forces applied by the user Therefore one can subtract the external force on an atom from the total force on this atom to get the pure force arising from the simulation system Note that enabletotalforces must be called first e loadmasses lt varname gt Loads requested atom and group masses in amu into a local array loadmasses should only be called from within the calcforces procedure For example loadcoords m and print m 4 e addforce lt atomid groupid gt lt force vector gt Applies force in kcal mol T to atom or group addforce should only be called from within the calcforces procedure For example addforce groupid 1 0 2 P e addenergy lt energy kcal mol gt This command adds the specified energy to the MISC column and hence the total energy in the energy output For normal runs the command does not affect the simulation trajectory at all and only has an artificial effect on its energy output However it can indeed affect minimizations With the commands above
336. tant lt Change the force constant towards this value gt Context harmonic Acceptable Values positive decimal Description When defined the current forceConstant will be moved towards this value during the simulation Time evolution of the force constant is dictated by the targetForceExponent parameter see below By default the force constant is changed smoothly over a total of targetNumSteps steps This is useful to introduce or remove re straints in a progressive manner If targetNumStages is set to a nonzero value the change is performed in discrete stages lasting targetNumSteps steps each This second mode may be used to compute the conformational free energy change associated with the restraint within the FEP or TI formalisms For convenience the code provides an estimate of the free energy derivative for use in TI A more complete free energy calculation particularly with regard to convergence analysis while not handled by the colvars module can be performed by post processing the colvars trajectory if colvarsTrajFrequency is set to a suitably small value It should be noted however that restraint free energy calculations may be handled more efficiently by an indirect route through the determination of a PMF for the restrained coordinate 22 e targetForceExponent lt Exponent in the time dependence of the force constant gt Context harmonic Acceptable Values decimal equal to or greater than 1 0 Default Value 1 0 Descrip
337. teger Default Value 2 Description Rather than only regenerating the pairlist at the beginning of a cycle regenerate multiple times in order to better balance the costs of atom migration pairlist generation and larger pairlists 90 e outputPairlists lt how often to print warnings gt Acceptable Values non negative integer Default Value 0 Description If an atom moves further than the pairlist tolerance during a simulation initially pairlistdist cutoff 2 but refined during the run any pairlists covering that atom are invalidated and temporary pairlists are used until the next full pairlist regeneration All interactions are calculated correctly but efficiency may be degraded Enabling outputPairlists will summarize these pairlist violation warnings periodically during the run e pairlistShrink lt tol 1 x on regeneration gt Acceptable Values non negative decimal Default Value 0 01 Description In order to maintain validity for the pairlist for an entire cycle the pairlist tolerance the distance an atom can move without causing the pairlist to be invalidated is adjusted during the simulation Every time pairlists are regenerated the tolerance is reduced by this fraction e pairlistGrow lt tol 1 x on trigger gt Acceptable Values non negative decimal Default Value 0 01 Description In order to maintain validity for the pairlist for an entire cycle the pairlist tolerance the distance an atom can move
338. temperature steps out of adaptTempTmin adaptTempTmax a random temperature in that range is assigned Otherwise the previous temperature is kept 179 12 3 Locally enhanced sampling Locally enhanced sampling LES 60 64 65 increases sampling and transition rates for a portion of a molecule by the use of multiple non interacting copies of the enhanced atoms These enhanced atoms experience an interaction electrostatics van der Waals and covalent potential that is divided by the number of copies present In this way the enhanced atoms can occupy the same space while the multiple instances and reduces barriers increase transition rates 12 3 1 Structure generation To use LES the structure and coordinate input files must be modified to contain multiple copies of the enhanced atoms psfgen provides the multiply command for this purpose NAMD supports a maximum of 255 copies which should be sufficient Begin by generating the complete molecular structure and guessing coordinates as described in Sec 4 As the last operation in your script prior to writing the psf and pdb files add the multiply command specifying the number of copies desired and listing segments residues or atoms to be multiplied For example multiply 4 BPTI 56 BPTI 57 will create four copies of the last two residues of segment BPTI You must include all atoms to be enhanced in a single multiply command in order for the bonded terms in the psf file to be duplicated co
339. tential thick line falls below a threshold energy E dashed line a boost potential is added The modified energy profiles thin lines have smaller barriers separating adjacent energy basins 11 1 Introduction NAMD is a parallel molecular dynamics program for UNIX platforms designed for high performance simulations in structural biology This document describes how to use NAMD its features and the platforms on which it runs The document is divided into several sections Section 1 gives an overview of NAMD Section 2 lists the basics for getting started Section 3 describes NAMD file formats Section 4 explains PSF file generation with psfgen Section 5 presents the potential functions non bonded interactions and full electrostatics Section 6 explains Generalized Born implicit solvent simulations Section 7 lists standard minimization and dynamics parameters Section 8 lists performance tuning parameters Section 9 explains user defined forces conformation change calculations Section 10 describes collective variable based calculations Section 11 explains alchemical free energy calculations Section 12 presents accelerated sampling methods Section 14 lists runtime analysis options Section 15 provides hints for X PLOR users Section 16 provides sample configuration files Section 17 gives details on running NAMD Section 18 gives details on installing NAMD 1 1 NAMD and molecular dynamics simulations Molecul
340. ter 191 pairInteractionCol parameter 191 pairInteractionFile parameter 191 pairInteractionGroup1 parameter 191 pairInteractionGroup2 parameter 191 pairInteractionSelf parameter 191 pairlistdist parameter 89 pairlistGrow parameter 91 pairlistMinProcs parameter 90 pairlistShrink parameter 91 pairlistsPerCycle parameter 90 pairlist Trigger parameter 91 parameters parameter 23 para TypeCharmm parameter 23 para TypeXplor parameter 23 parmfile parameter 28 patch psfgen command 41 pdb psfgen command 41 pdbalias atom psfgen command 44 pdbalias residue psfgen command 39 period colvars distanceZ keyword 143 PME parameter 51 PMEGridSizeX parameter 52 PMEGridSizeY parameter 52 PMEGridSizeZ parameter 52 PMEGridSpacing parameter 52 PMElInterpOrder parameter 51 PMEProcessors parameter 52 PMETolerance parameter 51 PRESSAVG 27 pressureProfile parameter 192 pressureProfileAtomTypes parameter 193 pressureProfileAtomTypesCol parameter 194 pressureProfileAtomTypesFile parameter 194 pressureProfileEwald parameter 193 pressureProfileEwaldX parameter 193 pressureProfileEwald Y parameter 193 pressureProfileEwaldZ parameter 193 pressureProfileFreq parameter 193 pressureProfileSlabs parameter 192 print command 16 psfcontext allcaps psfgen command 42 psfcontext create psfgen command 43 psfcontext delete psfgen command 43 psfcontext eval psfgen command 43 psfcontext mixedcase psfgen command 42 psfcontext psf
341. ter depends on the model so here we alias HOH to TIP3 Because CHARMM uses an additional H H bond we must disable generation of angles and dihedrals for segments containing water Then read the pdb file 8 Read water coordinates from PDB file Alias the atom type for water oxygen as well and read coordinates from the file to the segment SOLV Hydrogen doesn t show up in crystal structures so it is missing from this pdb file 9 Guessing missing coordinates The tolopogy file contains default internal coordinates which can be used to guess the locations of many atoms hydrogens in particular In the output pdb file the occupancy field of guessed atoms will be set to 0 atoms which are known are set to 1 and atoms which could not be guessed are set to 1 Some atoms are poorly guessed if needed bond lengths and angles were missing from the topology file Similarly waters with missing hydrogen coordinates are given a default orientation Write structure and coordinate files Now that all of the atoms and bonds have been created we can write out the psf structure file for the system We also create the matching coordinate pdb file The psf and pdb files are a matched set with identical atom ordering as needed by NAMD Using generated files in NAMD The files bpti pdb and bpti psf can now be used with NAMD but the initial coordinates require minimization first The following is an example NAMD configuration file for the BPTI example
342. terReference or rotateReference is on the gradients of some colvars include terms proportional to OR Ox rotational gradients and Ox Ox translational gradients By default these terms are calculated and included in the total gradients if this option is set to off they are neglected In the case of a minimum RMSD component this flag is automatically disabled because the contributions of those derivatives to the gradients cancel out e enableForces lt Apply forces from this colvar to this group gt Context atom group Acceptable Values boolean Default Value on Description If this option is off no forces are applied from this colvar to this group Other forces are not affected i e those from the MD engine from other colvars and other external forces For dummy atoms this option is off by default 10 3 3 Treatment of periodic boundary conditions In simulations with periodic boundary conditions NAMD maintains the coordinates of all the atoms within a molecule contiguous to each other i e there are no spurious jumps in the molecular bonds The colvar module relies on this when calculating a group s center of geometry but the condition may fail if the group spans different molecules in that case writing the NAMD output files wrapA11 or wrapWater could produce wrong results when a simulation run is continued from a previous one The user should then determine according to which type of colvars are being calculated w
343. th no loss of accuracy e useGrids lt Interpolate the hills with grids gt Context metadynamics Acceptable Values boolean Default Value on Description This option discretizes all hills for improved performance accumulating their energy and their gradients on two separate grids of equal spacing Grids are defined by the values of lowerBoundary upperBoundary and width for each colvar Currently this option is implemented for all types of variables except the non scalar types distanceDir or orientation If expandBoundaries is defined in one of the colvars grids are automatically expanded along the direction of that colvar e hillWidth lt Relative width of the hills gt Context metadynamics Acceptable Values positive decimal Default Value y27 2 Description Along each colvar the width of each Gaussian hill 2d is given by the product between this number and the colvar s width The default value gives hills whose 154 volume is the product of W times the width of all colvars For a smoother visualization of the free energy plot decrease width and increase hillWidth in the same proportion Note when useGrids is on default in most cases values smaller than 1 should be avoided to avoid discretization errors e rebinGrids lt Recompute the grids when reading a state file gt Context metadynamics Acceptable Values boolean Default Value off Description When restarting from a state file the grid s parameters bou
344. the constraint positions One also specifies such parameters as the force constant s for the constraints and the velocity with which the constraints move There are two major differences between SMD and harmonic constraints e In harmonic constraints each tagged atom is harmonically constrained to a reference point which moves with constant velocity In SMD it is the center of mass of the tagged atoms which is constrained to move with constant velocity e In harmonic constraints each tagged atom is constrained in all three spatial dimensions In SMD tagged atoms are constrained only along the constraint direction unless the optional SMDk2 keyword is used The center of mass of the SMD atoms will be harmonically constrained with force constant k SMDk to move with velocity v SMDVel in the direction 7 SMDDir SMD thus results in the following potential being applied to the system 1 S y 2 U F1 Fa t sh ot R t Ry a 33 Here t Ni dt where Nts is the number of elapsed timesteps in the simulation and dt is the size of the timestep in femtoseconds Also R t is the current center of mass of the SMD atoms and Ro is the initial center of mass as defined by the coordinates in SMDFile Vector is normalized by NAMD before being used Optionally one may also specify a transverse force constant k SMDk2 The potential then becomes ee ee sh ut R t Ro 0 Sho ee fa to Ro a 34 In this
345. the electrostic field of a charge distribution in a dielectric it is very expensive to solve and therefore not suitable for molecular dynamics 6 1 2 Generalized Born The Generalized Born GB equation is an approximation of the PBE It models atoms as charged spheres whose internal dielectric is lower than that of the environment The screening which each atom 7 experiences is determined by the local environment the more atom 7 is surrounded by other atoms the less it s electrostatics will be screened since it is more surrounded by low dielectric this property is called one atom descreening another Different GB models calculate atomic descreening differently Descreening is used to calculate the Born radius a of each atom The Born radius of an atom measures the degree of descreening A large Born radius represents small screening strong electric field as if the atom were in vacuum A small Born radius represents large screening weak electric field as if the atom were in bulk water The next section describes how the Born radius is calculated and how it is used to calculate electrostatics 6 1 3 Generalized Born Equations In a GB simulation the total electrostatic force on an atom 7 is the net Coulomb force on atom i from nearby atoms minus the GB force on atom i also caused by nearby atoms F ERRE pee 66 Forces are contributed by other nearby atoms within a cutoff The GB force on atom i is the derivative of the
346. the free energy gradient estimate and sampling histogram and the PMF in one dimensional calculations are appended to files on disk at the given time interval History file names use the same prefix as output files with hist appended e inputPrefix lt Filename prefix for reading ABF data gt Context abf Acceptable Values list of strings Description If this parameter is set for each item in the list ABF tries to read a gradient and a sampling files named lt inputPrefix gt grad and lt inputPrefix gt count This is done at startup and sets the initial state of the ABF algorithm The data from all provided files is combined appropriately Also the grid definition min and max values width need not be the same that for the current run This command is useful to piece together data from simulations in different regions of collective variable space or change the colvar boundary values and widths Note that it is not recommended to use it to switch to a smaller width as that will leave some bins empty in the finer data grid This option is NOT compatible with reading the data from a restart file colvarsInput option of the NAMD config file e applyBias lt Apply the ABF bias gt Context abf Acceptable Values boolean Default Value yes Description If this is set to no the calculation proceeds normally but the adaptive biasing force is not applied Data is still collected to compute the free energy gradient This is mostly int
347. the grid is defined for points 0 NV with a potential f i j k given by f i j k fo i fi fo N By shifting the images of the grid the potential can be transformed as illustrated in Fig 5 e mgridforcelite lt tag gt lt Is grid to use Gridforce Lite interpolation gt Acceptable Values yes or no Default Value no Description When Gridforce Lite is enabled a faster but less accurate interpolation method is used to compute forces Specifically rather than computing a tri cubic interpolation of the potential from which the force is then computed analytically Gridforce Lite computes force as a linear interpolation This method also increases the memory required by Gridforce Note that Gridforce Lite is incompatible with use of the mgridforcecont 123 keywords and with non uniform grids 9 4 Moving Constraints Moving constraints feature works in conjunction with the Harmonic Constraints see an appropriate section of the User s guide The reference positions of all constraints will move according to r t Fo vt 30 96 22 20 J Potential E 1 a l Unshifted Shifted S 6 amp 1 1 1 j 1 j 1 i jt 1 1 1 1 4 5 6 7 0 1 2 3 4 5 6 7 0 1 2 3 Grid index Figure 5 Graph showing a slice of a ramp potential with eight grid po
348. tion Sets the exponent a in the function used to vary the force constant as a function of time The force is varied according to a coupling parameter A raised to the power a ky ko A ky ko where ko ka and k are the initial current and final values of the force constant The parameter A evolves linearly from 0 to 1 either smoothly or in targetNumStages equally spaced discrete stages or according to an arbitrary schedule set with lambdaSchedule When the initial value of the force constant is zero an exponent greater than 1 0 distributes the effects of introducing the restraint more smoothly over time than a linear dependence and ensures that there is no singularity in the derivative of the restraint free energy with respect to lambda A value of 4 has been found to give good results in some tests e targetEquilSteps lt Number of steps discarded from TI estimate gt Context harmonic Acceptable Values positive integer Description Defines the number of steps within each stage that are considered equilibra tion and discarded from the restraint free energy derivative estimate reported reported in the output e lambdaSchedule lt Schedule of lambda points for changing force constant gt Context harmonic Acceptable Values list of real numbers between 0 and 1 Description If specified together with targetForceConstant sets the sequence of discrete A values that will be used for different stages 160 10 5 4 Linear re
349. to keep the cutoff set to the CHARMM prescribed value of 12 A The configuration options specific to MSM are listed below A simulation employing non periodic boundaries in one or more dimensions might have atoms that attempt to drift beyond the predetermined extent of the grid In the case that an atom does drift beyond the grid the simulation will be halted prematurely with an error message Several options listed below deal with defining the extent of the grid along non periodic dimensions beyond what can be automatically determined by the initial coordinates It is also recommended for non periodic simulation to configure boundary restraints to contain the atoms for instance through Tcl boundary forces in Sec 9 11 e MSM lt Use multilevel summation method for electrostatics gt 53 Acceptable Values yes or no Default Value no Description Turns on multilevel summation method MSMGridSpacing lt spacing between finest level grid points A gt Acceptable Values positive real Default Value 2 5 Description The grid spacing determines in part the accuracy and efficiency of MSM An error versus cost analysis shows that the best tradeoff is setting the grid spacing to a value close to the inter particle spacing The default value works well in practice for atomic scale simulation This value will be exact along non periodic dimensions For periodic dimensions the grid spacing must evenly divide the basis vector length the actua
350. tor defines the projection of the coordinates of a group of atoms or more pre cisely their deviations from the reference coordinates onto a vector in R where n is the number of atoms in the group The computed quantity is the total projection pb Ey Y vi Ult Xeog t Oxf 50 40 i 1 f where as in the rmsd component U is the optimal rotation matrix Xcog t and xe are the centers of geometry of the current and reference positions respectively and v are the components of the vector for each atom Example choices for v are an eigenvector of the covariance matrix essential mode or a normal mode of the system It is assumed that gt v 0 otherwise the colvars module centers the v automatically when reading them from the configuration As for the component rmsd the available options are atoms refPositionsFile refPositionsCol and refPositionsColValue and refPositions In addition the following are recognized e vector lt Vector components gt Context eigenvector Acceptable Values space separated list of x y z triplets Description This option mutually exclusive with vectorFile sets the values of the vector components e vectorFile lt PDB file containing vector components gt Context eigenvector Acceptable Values UNIX filename Description This option mutually exclusive with vector sets the name of a PDB file where the vector components will be read from the X Y and Z fields
351. tween atoms i and j in the reference structure If ro 7 is less than the Go cutoff distance the pairwise potential between atoms i and j is given by f oS a ofo V 6 07 a b 4 Golfi j Tij a ij rij i where ae is given as 2 ed f ne is greater than the Go cutoff distance the pair wise potential between atoms i and j is given by rep O 2 Vaolrij P o expRep Ae Neer UJ For each pairwise chain combination the following parameters are needed to define the Go potential e chaintypes 2 floats first_chain second_chain Defines the pairwise chain interaction 188 e epsilon 1 float e Determines the e constant of the Go potential in units of kcal mol A 2 e exp_a 1 integer a Determines the a constant for the Go potential e exp_b 1 integer b Determines the b constant for the Go potential e expRep 1 integer expRep Determines the expRep constant for the Go potential e sigmaRep 1 float 0 Determines the 0 constant for the Go potential in units of A e epsilonRep 1 float e P Determines the e P constant for the Go potential in units of kcal mol A e cutoff 1 float cutoff Defines the Go cutoff distance for this particular pairwise chain in units of A e Optional restriction 1 integer Determines if interactions between the i and i integer adjacent residue should be excluded Multiple restriction between
352. ult Value 4 0 4 0 4 0 Description The three components of this vector define three different cutoffs dy for each direction This option is mutually exclusive with cutoff e expNumer lt Numerator exponent gt Context coordNum Acceptable Values positive even integer Default Value 6 Description This number defines the n exponent for the switching function e expDenom lt Denominator exponent gt Context coordNum Acceptable Values positive even integer Default Value 12 Description This number defines the m exponent for the switching function e group2CenterOnly lt Use only group2 s center of mass gt Context coordNum Acceptable Values boolean Default Value off Description If this option is on only contacts between each atoms in group1 and the center of mass of group2 are calculated by default the sum extends over all pairs of atoms in group1 and group2 If group2 is a dummyAton this option is set to yes by default This component returns a dimensionless number which ranges from approximately 0 all in teratomic distances are much larger than the cutoff to Neroup1 X Ngroup2 all distances are less than the cutoff or Ngroup1 if group2CenterOnly is used For performance reasons at least one of group1 and group2 should be of limited size or group2CenterOnly should be used the cost of the loop over all pairs grows as Ngroup1 X Ngroup2 selfCoordNum coordination number between atoms within a group The selfCoor
353. uraged to experiment There should be no performance impact from enabling this feature e LJcorrection lt Apply long range corrections to the system energy and virial to account for neglected vdW forces gt Acceptable Values yes or no Default Value no Description Apply an analytical correction to the reported vdW energy and virial that is equal to the amount lost due to switching and cutoff of the LJ potential The correction will use the average of vdW parameters for all particles in the system and assume a constant homogeneous distribution of particles beyond the switching distance See 63 for details the equations used in the NAMD implementation are slightly different due to the use of a different switching function Periodic boundary conditions are required to make use of tail corrections LJcorrection as implemented is inconsistent with vdwForceSwitching 5 2 4 PME parameters PME stands for Particle Mesh Ewald and is an efficient full electrostatics method for use with periodic boundary conditions None of the parameters should affect energy conservation although they may affect the accuracy of the results and momentum conservation e PME lt Use particle mesh Ewald for electrostatics gt Acceptable Values yes or no Default Value no Description Turns on particle mesh Ewald e PMETolerance lt PME direct space tolerance gt Acceptable Values positive decimal Default Value 107 Description Affects the value of the
354. vars as scripted functions of components o ooo e 145 10 5 Biasing and analysis methods 2 a 146 10 5 1 Adaptive Biasing Force e 147 10 5 2 M tadynamics a 0 sae wk A a ee a aA 152 10 5 3 Harmonic r estraints seip rh A Soe ke ad O We ale BP EG WE BES 157 10 04 Linear restraints s po rapas a Bate A BS oe a et ee 161 10 5 5 Adaptive Linear Bias Experiment Directed Simulation 161 10 5 6 Multidimensional histograms 0 0 0 o 162 10 5 F Scripted bidsess 2 258 2402 Gs bo eo SR he HA es ee eS 163 10 6 Colvars Scripting 163 10 6 1 Managing the colvars module e 163 10 6 2 Input and output 24 4 8 sa a a aa ee 163 10 6 3 Accessing collective variables o ee 10 6 4 Accessing biases e 11 Alchemical Free Energy Methods 111 Theoretical Background y im a Bee eS A ee SR a eS 11 1 1 The dual topology paradigm 0 02000 pee ee 11 1 2 Free Energy Perturbation 0 000002 eee eee ee 11 1 3 Thermodynamic Integration 00 00 eee ee ee 11 2 Implementation of the free energy methods in NAMD 11 3 Examples of input files for running alchemical free energy calculations 11 4 Description of a free energy calculation output 2 e 11 4 1 Free Energy Perturbation 0002 eee eee 11 4 2 Thermodynamic Integration 0 0 0 e 12 Accelerated Sampling Methods 12 1
355. via the following options e extraBonds lt enable extra bonded terms gt Acceptable Values on or off Default Value off Description Specifies whether or not extra bonded terms are present e extraBondsFile lt file containing extra bonded terms gt Acceptable Values file Description File containing extra bonded terms May be repeated for multiple files The extra bonds file s should contain lines of the following formats e bond lt atom gt lt atom gt lt k gt lt ref gt e angle lt atom gt lt atom gt lt atom gt lt k gt lt ref gt e dihedral lt atom gt lt atom gt lt atom gt lt atom gt lt k gt lt ref gt e dihedral lt atom gt lt atom gt lt atom gt lt atom gt lt k gt lt n gt lt ref gt e improper lt atom gt lt atom gt lt atom gt lt atom gt lt k gt lt ref gt 64 e improper lt atom gt lt atom gt lt atom gt lt atom gt lt k gt lt n gt lt ref gt e lt comment gt In all cases lt atom gt is a zero based atom index the first atom has index 0 lt ref gt is a reference distance in bond or angle in degrees others and lt k gt is a spring constant in the potential energy function U x k x ref or for dihedrals and impropers with periodicity lt n gt specified and not 0 U x k 1 cos nz tref Note that ver is only a minimum for the harmonic potential the sinusoidal potential has minima at ref 180 n i x 360 n 65 6 Generali
356. wed with e g xmgrace output history and processed via awk or other tools There is also a script to load the output into VMD and color each frame according to replica index An example simulation folds a 66 atom model of a deca alanine helix in about 10ns replica namd is the master script for replica temperature exchange simulations To run 181 cd example mkdir output cd output mkdir 0 1 23 45 6 7 mpirun namd2 replicas 8 job0 conf stdout output d job0 d log mpirun namd2 replicas 8 job1 conf stdout output d job1 d log The number of MPI ranks must be a multiple of the number of replicas replicas Be sure to increment jobX for stdout option on command line show_replicas vmd is a script for loading replicas into VMD first source the replica exchange conf file and then this script then repeat for each restart conf file or for example just do vmd e load_all vmd This script will likely destroy anything else you are doing in VMD at the time so it is best to start with a fresh VMD clone_reps vmd provides the clone_reps commmand to copy graphical representation from the top molecule to all other molecules sortreplicas found in the namd2 binary directory is a program to un shuffle replica trajec tories to place same temperature frames in the same file Usage sortreplicas lt job_output_root gt lt num_replicas gt lt runs_per_frame gt final_step where job_output_root is the job specific output base
357. with multiple threads on either a single machine like a multicore build or across a network SMP builds combine multiple worker threads and an extra communication thread into a single process Since one core per process is used for the communication thread SMP builds are typically slower than non SMP builds The advantage of SMP builds is that many data structures are shared among the threads reducing the per core memory footprint when scaling large simulations to large numbers of cores SMP builds launched with charmrun use p to specify the total number of PEs worker threads and ppn to specify the number of PEs per process Thus to run one process with one commu nication and three worker threads on each of four quad core nodes one would specify 205 charmrun namd2 p12 ppn 3 lt configfile gt For MPI based SMP builds one would specify any mpiexec options needed for the required number of processes and pass ppn to the NAMD binary as mpiexec np 4 namd2 ppn 3 lt configfile gt See the Cray XE XK XC directions below for a more complex example 17 6 Cray XE XK XC First load modules for the GNU compilers XE XK only XC should use Intel topology informa tion huge page sizes and the system FFTW 3 library module swap PrgEnv cray PrgEnv gnu module load rca module load craype hugepages8M module load fftw The CUDA Toolkit module enables dynamic linking so it should only be loaded when building CUDA binaries and never fo
358. without causing the pairlist to be invalidated is adjusted during the simulation Every time an atom exceeds a trigger criterion that is some fraction of the tolerance distance the tolerance is increased by this fraction e pairlistTrigger lt trigger is atom beyond 1 x tol gt Acceptable Values non negative decimal Default Value 0 3 Description The goal of pairlist tolerance adjustment is to make pairlist invalidations rare while keeping the tolerance as small as possible for best performance Rather than monitoring the very rare case where atoms actually move more than the tolerance distance we reduce the trigger tolerance by this fraction The tolerance is increased whenever the trigger tolerance is exceeded as specified by pairlistGrow 91 9 User Defined Forces There are several ways to apply external forces to simulations with NAMD These are described below 9 1 Constant Forces NAMD provides the ability to apply constant forces to some atoms There are three parameters that control this feature e constantForce lt Apply constant forces gt Acceptable Values yes or no Default Value no Description Specifies whether or not constant forces are applied e consForceFile lt PDB file containing forces to be applied gt Acceptable Values UNIX filename Description The X Y Z and occupancy O fields of this file are read to determine the constant force vector of each atom which is X Y Z O in unit of kcal
359. y replica or global e replicaEval replica script e replicaYield seconds e replicaDcdFile index off filename The key can be any string By default the checkpoint is stored in the memory of the replica the command is called on If you specify a replica index the checkpoint is stored asynchronously in that replica s memory If you specify global a hash is computed based on the key to select the replica on which to store the checkpoint You can have checkpoints with the same key stored on multiple replicas at once if you really want to The checkpoint commands will not return until the checkpoint operation has completed 19 Storing checkpoints is not atomic If two replicas try to store a checkpoint with the same key on the same replica at the same time you may end up with a mix of the two and probably duplicate missing atoms If one replica tries to load a checkpoint while another replica is storing it the same may happen You cannot store a checkpoint on a replica until that replica has created its own patch data structures This can be guaranteed by calling startup and replicaBarrier before any remote checkpoint calls The replicaEval command asynchronously executes its script in the top level context of the target replica s Tcl interpreter and returns the result or error This should be general enough to build any kind of work scheduler or shared data structure you need If you want to call replicaE val repe
360. y NAMD during a previous simu lation Either the temperature or the velocities binvelocities option must be defined to determine an initial set of velocities Both options cannot be used together e binvelocities lt binary velocity file gt Acceptable Values UNIX filename Description The binary file containing initial velocities for all atoms in the simulation A binary velocity file is created as output from NAMD by activating the binaryrestart or binaryoutput options The binvelocities option should be used as an alternative to velocities Either the temperature or the velocities binvelocities option must be defined to determine an initial set of velocities Both options cannot be used together e bincoordinates lt binary coordinate restart file gt Acceptable Values UNIX filename Description The binary restart file containing initial position coordinate data A binary coordinate restart file is created as output from NAMD by activating the binaryrestart or binaryoutput options Note that in the current implementation at least the bincoordinates option must be used in addition to the coordinates option but the positions specified by coordinates will then be ignored e cwd lt default directory gt Acceptable Values UNIX directory name Description The default directory for input and output files If a value is given all filenames that do not begin with a are assumed to be in this directory For example if cwd is set to scr
361. y integrated and a potential of mean force is written under the file name lt outputName gt pmf in a plain text format that can be read by most data plotting and analysis programs e g gnuplot In dimension 2 or greater integrating the discretized gradient becomes non trivial The stan dalone utility abf_integrate is provided to perform that task abf_integrate reads the gradient data and uses it to perform a Monte Carlo M C simulation in discretized collective variable space specifically on the same grid used by ABF to discretize the free energy gradient By default a history dependent bias similar in spirit to metadynamics is used at each M C step the bias at the current position is incremented by a preset amount the hill height Upon convergence this bias counteracts optimally the underlying gradient it is negated to obtain the estimate of the free energy surface abf_integrate is invoked using the command line integrate lt gradient_file gt n lt nsteps gt t lt temp gt m 011 h lt hill_height gt f lt factor gt 151 The gradient file name is provided first followed by other parameters in any order They are described below with their default value in square brackets e n number of M C steps to be performed by default a minimal number of steps is chosen based on the size of the grid and the integration runs until a convergence criterion is satisfied based on the RMSD between the target gradien
362. y notify Illinois in writing Licensee expressly agrees to use the Software only in the manner and for the specific uses authorized in this Agreement 5 By using or copying this Software Licensee agrees to abide by the copyright law and all other applicable laws of the U S including but not limited to export control laws and the terms of this license Illinois shall have the right to terminate this license immediately by written notice upon Licensee s breach of or non compliance with any of its terms Licensee may be held legally responsible for any copyright infringement that is caused or encouraged by its failure to abide by the terms of this license Upon termination Licensee agrees to destroy all copies of the Software in its possession and to verify such destruction in writing 6 The user agrees that any reports or published results obtained with the Software will ac knowledge its use by the appropriate citation as follows NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana Champaign Any published work which utilizes NAMD shall include the following reference James C Phillips Rosemary Braun Wei Wang James Gumbart Emad Tajkhorshid Elizabeth Villa Christophe Chipot Robert D Skeel Laxmikant Kale and Klaus Schul ten Scalable molecular dynamics with NAMD Journal of Computational Chemistry 26 1781 180
363. y output filename gt Acceptable Values filename Default Value outfilename Description An output file named alchOutFile containing the FEP energies or tiOutFile containing the TI derivatives dumped every alchOutFreq steps alchVdwShiftCoeff lt Soft core van der Waals radius shifting coefficient gt Acceptable Values positive decimal Default Value 5 Description This is a radius shifting coefficient of A that is used to construct the modified vdW interactions during alchemical free energy calculations Providing a positive value for alchVdWShiftCoeff ensures that the vdW potential is finite everywhere for small values of A which significantly improves the accuracy and convergence of FEP and TI calculations and also prevents overlapping particles from making the simulation unstable During FEP and TI assuming A 0 denotes an absence of interaction the interatomic distances used in the Lennard Jones potential are shifted according to 7 47 r r alchVdWShiftCoeff x 1 2 alchElecLambdaStart lt Value of to introduce electrostatic interactions gt Acceptable Values positive decimal Default Value 0 5 Description In order to avoid the so called end point catastrophes it is crucial to avoid situations where growing particles overlap with existing particles with an unbounded interaction potential which would approach infinity as the interaction distance approaches zero 7 17 One possible route for avoidi
364. y reproduce the PME results 32 At this time we discourage use of the higher order interpolation schemes Hermite quintic etc as they are still under development With cubic interpolation MSM now gets roughly half the performance of PME Comparable performance and better scaling for MSM have been observed with the optimizations described in Ref 32 which will be available shortly For now NAMD s implementation of the MSM does not calculate the long range electrostatic contribution to the virial so use with a barostat for constant pressure simulation is inappropriate Note that the experiments in Ref 32 involving constant pressure simulation with MSM made use of a custom version that is incompatible with some other NAMD features so is not yet available The performance of PME is generally still better for smaller systems with smaller processor counts MSM is the only efficient method in NAMD for calculating full electrostatics for simulations with semi periodic or non periodic boundaries The periodicity is defined through setting the cell basis vectors appropriately as discussed in Sec 7 The cutoff distance discussed earlier in this section also determines the splitting distance between the MSM short range part calculated exactly and long range part interpolated from the grid hierarchy this splitting distance is the primary control for accuracy for a given interpolation and splitting although most simulations will likely want
365. y runs The DCDfile may be changed to write binary coordinate tra jectory output to separate files The restartname may be changed to write restart output to separate files The checkpoint and revert commands no arguments allow a scripted simulation to save and restore in memory to a single prior state The output and reinitatoms commands support multiple saved states using files Multiple saved states in memory are supported by the commands checkpointStore checkpointLoad checkpointSwap and checkpoint Free all of which take a string key as an argument plus an optional second argument that is either replica index the checkpoint is stored asynchronously on the target replica or the keyword global the target replica is computed as a hash of the key The output command takes an output file basename and causes coor vel and xsc files to be written with that name Alternatively output withforces and output onlyforces will write a force file either in addition to or instead of the regular files The reinitatoms command reinitializes coordinates velocities and periodic cell dimensions to those initially read in random velocities are generated if they were not read from a file An optional file basename argument matching that passed to the output command causes coor vel and xsc files to be read assuming the format indicated by the binaryoutput parameter
366. ymmetryk entry for details symmetryFirstFullStep lt First step to apply full harmonic force gt Acceptable Values Non negative integer Default Value symmetryFirstStep Description Force constant symmetryk linearly increased from symmetryFirstStep to symmetryFirstFullStep symmetryLastFullStep lt Last step to apply full harmonic force gt Acceptable Values Non negative integer Default Value symmetryLastStep Description Force constant symmetryk linearly decreased from symmetryLastFullStep to symmetryLastStep symmetryk lt Constant for harmonic restraining forces gt Acceptable Values Positive value Description Harmonic force constant Scaled down by number of atoms in the monomer If this setting is omitted the value in the occupancy column of the pdb file specified by symmetrykFile will be used as the constant for that atom This allows the user to specify the constant on a per atom basis symmetrykFile lt pdb containing per atom force constants gt Acceptable Values Path to pdb file Description pdb where the occupancy column specifies the per atom force constants If using overlapping symmetry groups you must include one additional symmetrykfile per symmetryFile 99 e symmetryScaleForces lt Scale symmetry restraints over time gt Acceptable Values on or off Default Value off Description If turned on the harmonic force applied by the symmetry re straints will linearly evolve with each time step based
367. ystem is a function of the general extent parameter A which connects smoothly state a to state b In the simplest case such a connection may be achieved by linear combination of the corresponding Hamiltonians H X Pz A Ho x px AHy x Px 1 A Ha x Pz 57 where Ha x Pz describes the interaction of the group of atoms representative of the reference state a with the rest of the system Hj x Px characterizes the interaction of the target topology b with the rest of the system Ho x p is the Hamiltonian describing those atoms that do not undergo any transformation during the MD simulation For instance in the point mutation of an alanine side chain into that of glycine by means of a free energy calculation either free energy perturbation or thermodynamic integration the topology of both the methyl group of alanine and the hydrogen borne by the Ca in glycine co exist throughout the simulation see Figure 7 yet without actually seeing each other The energy and forces are defined as a function of A in such a fashion that the interaction of the methyl group of alanine with the rest of the protein is effective at the beginning of the simulation i e A 0 while the glycine Ca hydrogen atom does not interact with the rest of the protein and vice versa at the end of the simulation i e A 1 For intermediate values of A both the alanine The features described in this section were contributed by Surjit B Dixit Ch
368. zed Born Implicit Solvent Generalized Born implicit solvent GBIS is a fast but approximate method for calculating molecular electrostatics in solvent as described by the Poisson Boltzmann equation which models water as a dielectric continuum GBIS enables the simulation of atomic structures without including explicit solvent water The elimination of explicit solvent greatly accelerates simulations this speedup is lessed by the increased computational complexity of the implicit solvent electrostatic calculation and a longer interaction cutoff These are discussed in greater detail below 6 1 Theoretical Background Water has many biologically necessary properties one of which is as a dielectric As a dielectric water screens lessens electrostatic interactions between charged particles Water can therefore be crudely modeled as a dielectric continuum In this manner the electrostatic forces of a biological system can be expressed as a system of differential equations which can be solved for the electric field caused by a collection of charges 6 1 1 Poisson Boltzmann Equation The Poisson Boltzmann equation PBE is a nonlinear equation which solves for the electrostatic field W 7 based on the position dependent dielectric e r the position dependent accessibility of position F to the ions in solution A F the solute charge distribution p F and the bulk charge density c of ion q While this equation does exactly solve for

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