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1. 7 7 gives the distance between the pair of atoms The parameter Emin Urs Rmin is the minimum of the 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 contrib
2. units used for output 23 upperBoundary parameter 94 upperWallConstant parameter 95 useConstantArea parameter 64 useConstantRatio parameter 64 useDPME parameter 48 useFlexibleCell parameter 64 useGrids parameter 113 156 useGroupPressure parameter 64 useSettle parameter 50 vdwGeometricSigma parameter 45 velDCDfile parameter 22 velDCDfreq parameter 23 velocities parameter 20 velocityQuenching parameter 57 width parameter 94 wrapAll parameter 54 wrapNearest parameter 54 wrapWater parameter 54 writeHillsTrajectory parameter 115 writepdb psfgen command 40 writepsf psfgen command 39 XSTfile parameter 53 XSTfreq parameter 53 zeroMomentum parameter 58
3. 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 GROMACS 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 27 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 extr
4. e oneSiteSystemForce lt dihedral Measure system force on group 1 only gt Acceptable Values boolean Default Value no Description If this is set to yes the system force is measured along a vector field see equation 23 in section 9 3 1 that only involves atoms of group1 See section 9 3 1 for an example Component 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 27 This function is summed over all pairs of atoms in group1 and group2 A oN 1 C groupt group2 Y D 1Egroup1 Egroup2 xi x31 do Ix x do 13 This colvar component accepts the same options as distance group1 and group2 In addition to them it recognizes the following options e cutoff lt coordnum Reference distance A gt 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 dy it has a value of n m 1 2 with the default n and m and at d gt dy it goes to zero approximately like d Hence for a proper behavior m must be larger than n e expNumer lt coordnum Nume
5. 119 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 10 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 Each keyword has two variants one that is used in FEP calculations and a second that should be used when performing TI The FEP and TI variants are seperated by slashes like so fepKeyword tiKeyword listing first the FEP keyword and second the TI keyword The FEP and TI specific keywords should be used exclusively with FEP or TI respectively and should not be intermixed during a simulation e fep thermInt lt Is an alchemical free energy perturbation to be performed gt Acceptable Values on or off Default Value off Description Turns on alchemical tra
6. 15 4 SGI Altix Be sure that the MPI_DSM_DISTRIBUTE environment variable is set then use the Linux Itanium MPI Altix version of NAMD along with the system mpirun mpirun np lt procs gt lt configfile gt 15 5 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 15 6 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 of 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 146 15 7 Improving Parallel Scaling While N
7. 16 M P Allen and D J Tildesley Computer Simulation of Liquids Oxford University Press New York 1987 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 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 112 535 542 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 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 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
8. 217 244 6078 Contents 1 Introduction 1 1 NAMD and molecular dynamics simulations 1 2 User feedback 1 3 Acknowledgments Getting Started 2 1 What is needed 2 2 NAMD configuration file Configuration parameter syntax 1 e a Tcl scripting interface and features o oo oo 2 2 3 Required NAMD configuration parameters 2 2 1 2222 Input and Output Files 3 1 Eile formats s io A Boe ee a a ee A ee 3 11 PDB files Tira 2c bp Sk eee RE a De A a a ana 31 22 X PLOR format PSF Mesy sos gk hae Poke Spe ade A a ee ee SHES 3 13 CHARMM19 CHARMM22 and CHARMM27 parameter files 3 4 DCD trajectory Mes se cc oe ee be ee Ey ak ae 3 2 NAMD configuration parameters 2 0 ee ee 32 1 Inputfiles ta obi pte ele be ae SUM eh oe hoe aad 322 OUTPUT ce a ee a eee nh ee at 3 2 3 Standard Output Sma mega aa a e ee a a 3 3 AMBER force field parameters eee ee 3 4 GROMACS force field parameters 2 0 0 0 0 0202 ee eee Creating PSF Structure Files 4 1 Ordinary Usagre fs GE Sit pe be A ge es AS ed 4 1 1 Preparing separate PDB files 0 o e 4 1 2 Deleting unwanted atoms 000002 eee ee 4 2 BPTI Example eur bcd ea ee a hae ee BAe Pee eee eee a 4 3 Building solvent around a protein 2 aa ee 4 4 List of Commands 2 0 0 0 ee ee 4 5 Example of a Session Log potaa a oe uoa KE i e EE E A Force Field Parameters 5 1 Potential energy functions o
9. NAMD User s Guide Version 2 7b1 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 N Krawetz S Kumar D Kunzman C Lee C Mei M Nelson J Phillips O Sarood A Shinozaki G Zheng F Zhu May 27 2009 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 2 7b1 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 N Krawetz S Kumar D Kunzman C Lee C Mei M Nelson J Phillips O Sarood A Shinozaki G Zheng F Zhu Theoretical Biophysics Group Beckman Institute University of Illinois 1995 2002 The Board of Trustees of the University of Illinois All Rights Reserved NAMD Molecular Dynamics Software Non Exclusive Non Commercial Use License Introduction The University of Illino
10. gradients are computed In the direction of each colvar the grid ranges from lowerBoundary to upperBoundary and the bin width grid spacing is set by the width parameter 110 Output files The ABF bias produces the following files all in multicolumn ASCII format e lt outputName gt grad current estimate of the free energy gradient grid in multicolumn e lt outputName gt count total number of samples collected on the same grid e lt outputName gt 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 lt outputName gt 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 NAMD run of 0 steps is enough Reconstructing a multidimensional free energy surface If a one dimensional calculation is performed the estimated free energy gradient is automatically 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
11. 72 8 3 Grid Forces NAMD provides the ability to specify grids describing an electrical potential in the simulation space Each atom is affected by the potential based on its charge and its position interpolated from the specified grid s Energy due to the grid defined field will be reported in the MISC column of the output 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 format 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 xn yn and zn are the number of data points along each axis 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 Note Other features of the DX file format are not handled by this code HH HH HH HH HOH OF OF OF ob
12. 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 pressureProfileEwaldX 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 0 135 coorfile close 136 13 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 bot
13. Enable soft core vdW potential tiElecLambdaStart 0 1 Introduce electrostatics for lambda gt 0 1 tiLambda 0 run 10000 tiLambda 0 00001 run 10000 tiLambda 0 0001 run 10000 tiLambda 0 001 run 10000 tiLambda 0 01 run 10000 set Lambda 0 1 while Lambda lt 0 9 4 tiLambda Lambda run 10000 set Lambda expr Lambda 0 1 tiLambda 0 99 run 10000 tiLambda 0 999 run 10000 tiLambda 0 9999 run 10000 124 tiLambda 0 99999 run 10000 tiLambda 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 VdWShiftCoeff parameter delayed introduction of electrostatics with a non zero tiElecLambdaStart value and very gradual scaling of A towards its end points 10 4 Description of a free energy calculation output 10 4 1 Free Energy Perturbation When running FEP the fepOutFile contains electrostatic and van der Waals energy data cal culated for lambda and lambda2 written every fepOutFreq 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 fepEquilSteps steps the calculation of dE_avg and dG is restarted The accumulated net free energy change is written at each lambda value and at the end of the s
14. 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 that 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 holdin
15. 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 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 23 Description The number of timesteps between each pressure ou
16. colvarsConfig e colvarsConfig lt Configuration file for the collective variables gt Acceptable Values UNIX filename Description This file contains the definition of all collective variables and their biasing or analysis methods It is meant to contain all the information that the user provides at the beginning of a simulation In the case that additional information is needed to continue a simulation run such information is read from the file provided by colvarsInput 90 e colvarsInput lt Input state file for the collective variables gt Acceptable Values UNIX filename Description When continuing a previous simulation run this file contains the information regarding the current state of all collective variables and their biasing methods The format of this file is similar to that of colvarsConfig but the set of keywords and their meaning are different In normal circumstances this file is written automatically at the end of a previous simulation and the user does not need to modify it Othe parameters defining a collective variables calculation are not read from the NAMD con figuration file but from a separate file As a consequence keywords described in the following sections are not NAMD keywords 9 1 2 Output files By default the collective variables module writes three output files e a state file named lt outputName gt colvars state this file is in ASCII format regardless of the value of binaryOutput in the NAM
17. e hillWidth lt metadynamics Relative width of the hills gt Acceptable Values positive decimal Default Value 3 0 Description Along each colvar the width of each gaussian 2d is given by the product between this number and the colvar s width Values larger than 1 act as a smoothing parameter Values smaller than 1 should be avoided in particular when useGrids is on in order to avoid large errors in the discretization e multipleReplicas lt metadynamics Multiple replicas metadynamics gt Acceptable Values boolean Default Value off Description If this option is on multiple independent replica of the same system can be simulated at the same time and share the same hills 37 This is achieved by letting each replica save its newly created hills to the file lt outputName gt colvars lt name gt lt replicaID gt hills the path to it is communicated to the other replicas through the file replicaFilesRegistry shared by all replicas Every replicaUpdateFrequency steps each replica reads the new hills created by the other replicas and adds them to its own e replicaID lt metadynamics Set the identifier for this replica gt Acceptable Values string Description If multipleReplicas is on this option sets a unique identifier for this replica Hence when simulating with more than one replica different colvars configuration files with different values for this option should be used e replicaFilesRegistry l
18. 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 pairInteractionGroupi 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 2 132 12 2 Pressure profile calculations NAM
19. for each colvar and intrinsic constraints to the colvar value For example when moving the restraint center of a dihedral the total movement in a single run will be at most 180 a rotation of 210 will be interpreted as one of 150 if a complete 360 turn of a dihedral is desired multiple runs at least two with different targets should be used When continuing 115 a simulation run the centers specified in the configuration file lt colvarsConfig gt will be overridden by those saved in the state file lt colvarsInput gt e targetsNumSteps lt harmonic Number of steps for steering gt Acceptable Values positive integer Default Value 0 Description If larger than zero it defines the number of steps required to move the restraint centers towards the specified targets After the targets have been reached the centers are maintained fixed To perform Steered Molecular Dynamics SMD simulations on the colvars implemented in this module it is sufficient to set a desired set of colvar target in the harmonic block and enable outputAppliedForce within the configuration block of each of the colvars involved 9 3 4 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 common pa
20. in amu into a local array loadmasses should only be called from within the calcforces procedure For example loadcoords m and print m 4 82 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 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
21. ischrgd 1 NAMD doesn t force neutralization of charge amp end 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 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 26 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 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
22. lt metadynamics Frequency of update of the grids gt Acceptable Values positive integer Default Value newHillFrequency Description When useGrids is on all the newly created hills are projected onto the two grids every gridsUpdateFrequency steps e dumpFreeEnergyFile lt metadynamics Periodically save the PMF gt Acceptable Values boolean Default Value on Description When useGrids and this option are on the PMF is written every 113 colvarsRestartFrequency steps to the file lt outputName gt pmf If there is more than one metadynamics bias active the name of this bias is included in the file name e saveFreeEnergyFile lt metadynamics Keep all the PMF files gt Acceptable Values boolean Default Value off Description When dumpFreeEnergyFile and this option are on the step number is included in the file name Activating this option can be useful to qualitatively assess the convergence of the simulation by comparing PMFs at different times e expandGrids lt metadynamics Automatically expand the grids gt Acceptable Values boolean Default Value off Description When useGrids and this option are on each time a colvar comes close to the grid boundaries these are expanded so that there is always a buffer amounting to three times a gaussian width The new grids have the same spacing as the original ones and the new boundaries are saved in the state file which overrides the values from the configuration file
23. runs per frame the number of runs between trajectory outputs frames_per restart the number of frames between restart outputs namd_config file the NAMD config file containing all parameters needed for the simulation except seed langevin langevinDamping langevinTemp outputEnergies outputnane dcdFreq temperature bincoordinates binvelocities or extendedSystem which are provided by replica exchange tcl output_root the directory fileroot for output files psf_file the psf file for show_replicas vmd initial_pdb_file the initial coordinate pdb file for show_replicas vmd fit_pdb file the coodinates that frames are fit to by show_replicas vmd e g a folded structure server_port the port to connect to the replica server on and spawn _namd_command a command from spawn_namd tcl and arguments to launch NAMD jobs The lib replica example directory contains all files needed to fold a 66 atom model of a deca alanine helix alanin_base namd basic config options for NAMD alanin params parameters alanin psf structure unfolded pdb initial coordinates 130 alanin pdb folded structure for fitting in show_replicas vmd fold_alanin conf config file for replica_exchange tcl script restart_1 conf config file to continue alanin folding another 10 ns and load_all vmd load all output into VMD and color by target temperature The fold_alanin conf config file contains the following settings set set set
24. 16 cellBasisVectorl parameter 53 cellBasisVector2 parameter 53 cellBasisVector3 parameter 53 cellOrigin parameter 53 centerReference parameter 104 centers parameter 115 checkpoint command 17 colvars parameter 90 108 colvarsConfig parameter 90 colvarsInput parameter 91 152 colvarsRestartFrequency parameter 93 colvarsTrajFrequency parameter 92 COMmotion parameter 58 componentCoeff parameter 102 componentExp parameter 102 consexp parameter 50 consForceFile parameter 72 consForceScaling parameter 72 conskcol parameter 50 conskfile parameter 50 consref parameter 50 constantForce parameter 72 constraints parameter 50 constraintScaling parameter 51 coord psfgen command 39 coordinates parameter 20 coordpdb psfgen command 39 coorfile command 17 corrFunc parameter 106 corrFuncLength parameter 107 corrFuncNormalize parameter 106 corrFuncOffset parameter 107 corrFuncOutputFile parameter 107 corrFuncStride parameter 107 corrFuncType parameter 106 corrFuncWithColvar parameter 106 cutoff parameter 43 98 cutoff3 parameter 98 cwd parameter 21 cylindricalBC parameter 55 cylindricalBCAxis parameter 55 cylindricalBCCenter parameter 55 cylindricalBCexp1 parameter 56 cylindricalBCexp2 parameter 56 cylindricalBCk1 parameter 56 cylindricalBCk2 parameter 56 cylindricalBCl1 parameter 56 cylindricalBCl2 parameter 56 cylindricalBCr1 parameter 55 cylindricalBCr2 parameter 56 DCDfile parame
25. Multiple timestep parameters ooo a eee ee eee 6 4 Temperature Control and Equilibration o ooo 6 4 1 Langevin dynamics parameters 6 4 2 Temperature coupling parameters 0 2 00 00 004 G 6 4 3 Temperature rescaling parameters 02 0 0000 2 e ee 6 4 4 Temperature reassignment parameters 0 000000 eee 6 5 Pressure Control hw aon gh we heh ah OHO el A ne A hoy eae webb 6 5 1 Berendsen pressure bath coupling 02 02 20004 6 5 2 Nos Hoover Langevin piston pressure control 2 4 Performance Tuning 7 1 Non bonded interaction distance testing 1 soo e e ee User Defined Forces 8 1 Constant Forces sia a a oree a be ea eee ee ee 8 2 External Electric Field 2 2 ee 8 3 GridvHOrees ss xe bye Taig Rete okies p Boos Gees E ke AE EP oh se DES 8 4 Moving Constraints eq 2 fo ere a e E A ee Ae yl Ee 8 5 Rotating Constraints s 4 cele ak a Bake eo eae a eb Sed Bee 8 6 Targeted Molecular Dynamics TMD visceral OSG ee ek ee aoe A RS 8 7 Steered Molecular Dynamics SMD e 8 8 Interactive Molecular Dynamics IMD lt lt 8 9 Tcl Forces and Analysis 8 10 Tel Boundary Forces sa s Senaosa ba a a ee ee 8 11 External Program Forces ie os so accs ap mte oni ae aa a i Sa E a a e RSE a 53 53 53 54 55 56 56 57 57 57 58 58 59 61 61 62 62 63 63 65 65 68 68 9 Collective
26. The switching function used is based on the X PLOR switching function The parameter switchdist specifies the distance 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 mean
27. 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 that 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 6 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 58 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
28. Variable based Calculations 9 1 General parameters and input output files o o o o ooo 9 1 1 NAMD parameters 9 1 2 Output files 64 224 sa fk ra a ee ee ee ee 9 1 3 Colvars module configuration file o e 9 2 Declaring and using collective variables o o e eee eee 9 2 1 Collective variable components 0 000000 eee ee eee 9 2 2 Linear and polynomial combinations of components 9 2 3 Defining atom groups 9 2 4 Statistical analysis of individual collective variables 9 3 Biasing and analysis methods 0 0 0002 eee ee ee eee 9 3 1 Adaptive Biasing Force calculations o e 9 3 2 Metadynamics calculations o e 9 3 3 Harmonic restraints and Steered Molecular Dynamics 9 3 4 Multidimensional histograms a 10 Alchemical Free Energy Methods 102 Theoretical Backeround es ii ic got hk a AA A doo ai Bd 10 1 1 The dual topology paradigm 0 0 02 000 eee ee 10 1 2 Free Energy Perturbation 2 0 0 0 0 000 2 ee ee ee 10 1 3 Thermodynamic Integration 2 2 0 0 000 eee ee 10 2 Implementation of the free energy methods in NAMD 10 3 Examples of input files for running alchemical free energy calculations 10 4 Description of a free energy calculation output 2 20 2 00000 eee 10 4 1 Free Energy Perturbation 0 0 000002
29. Vineta is a good approximant of the free energy A and the only dependence on the specific conformational history 0t 20t is by an irrelevant additive constant A amp Vmnetal k 26 Provided that the set of collective variables fully describes the relevant degrees of freedom the accuracy of the reconstructed profile is a function of the ratio between W and t 10 For the optimal choice of d and D the diffusion constant of the variable see reference 10 As a rule of thumb the very upper limit for the ratio W t is given by kpT Tg where TE is the longest among 112 s correlation times In the most typical conditions to achieve a good statistical convergence the user would prefer to keep W t much smaller than kgT Tg Given A the extension of the free energy profile along the colvar and A A amp the highest free energy that needs to be sampled e g that of a transition state the upper bound for the required simulation time is of the order of Ns A A W2d multiples of t When several colvars are used the upper bound amounts to Ns 1 x Ns 2 x x NslEn X t In metadynamics runs performed with this module the parameter d for each hill eq 25 is chosen as half the width of the corresponding colvar amp while all the other parameters must be provided within the metadynamics block In addition to the colvars option to lis
30. atom group Atoms within a number range gt Acceptable Values lt Starting number gt lt Ending number gt Description This option adds to the group all the atoms whose numbers are within the range specified It can be used multiple times for the same group Atom numbering starts from 1 May be repeated atomNameResidueRange lt atom group Named atoms within a range of residue numbers gt 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 range provided May be repated psfSegID lt atom group PSF segment identifier gt Acceptable Values string max 4 characters Description This option sets the PSF segment identifier for all instances of atomNameResidueRange within this atom group This option need not be provided when non PSF topologies are used by NAMD atomsFile lt atom group PDB file name for atom selection gt Acceptable Values string Description This option selects atoms from the PDB file provided and adds them to the group according to the value in the column atomsCol Note the PDB file provide must match the number of atoms in the topology atomsCol lt atom group PDB column to use for the selection gt Acceptable Values X Y Z 0 or B Default Value 0 103 Description This option specifies which column in atomsFile is used to determine the atoms to be includ
31. 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 writepsf 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 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 and PDB files This command also exists under the deprecated name alias Arguments lt alternate name gt Residue name found in PDB file lt real name gt Residue name found in topology file Context Before reading sequen
32. 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 156 472 477 1989 C Chipot and D A Pearlman Free energy calculations the long and winding gilded road Mol Sim 28 1 12 2002 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 and A Pohorille Calculating free energies using average force J Chem Phys 115 20 9169 9183 NOV 22 2001 149 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 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
33. 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 138 14 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 20 139 This file is again for alanin but shows a slightly more 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
34. group gt Acceptable Values atoms block Description Defines the group of atoms of which the RMSD should be calculated e refPositions lt rmsd Reference coordinates gt Acceptable Values space separated list of x y x triplets Description This option mutually exclusive with refPositionsFile sets the reference coordinates to be compared with The list should be as long as the atom group atoms This option is independent from that with the same keyword within the atoms block 99 e refPositionsFile lt rmsd Reference coordinates file gt 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 of the PDB file is the same as that provided by refPositionsFile within the atoms block but is independent from that with the same keyword within the atoms block e refPositionsCol lt rmsd PDB column to use gt Acceptable Values X Y Z 0 or B Default Value 0 Description If refPositionsFile is defined and the file contains all the atoms in the topology this option sets which PDB field is used to select the reference coordinates for atoms Otherwise this field is ignored e refPositionsColValue lt rmsd Value in the PDB column gt Acceptable Values positive decimal Description If defined this value identifies in the PDB column refPositionsCol of the file refPositionsFile whic
35. 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 cylindricalBC11 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 e cylindricalBCri 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 55 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 f
36. implementation relies partly on the classic formulation 11 and partly on a more versatile scheme originating in a work by Ruiz Montero et al 39 generalized by den Otter 18 and extended to multiple variables by Ciccotti et al 14 Consider a system subject to constraints of the form 0 x 0 Let v4 ief1 n be arbitrarily chosen vector fields RIN RIN verifying for all i j and k Vi Vej 05 21 Vi Ve Ok 0 22 then the following holds 14 OA DE vi Vz V kBT Ve vijg 23 where V 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 11 Condition 21 states that the direction along which the system force on is measured is orthogonal to the gradient of which means that the force measured on does not act on Equation 22 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 3 1 In the framework of ABF F is accumulated in bins of finite size 0 thereby p
37. 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 51 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 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 O indicates that the atom is not fixed 52 6 Standard Minimiza
38. lt resid gt Name of residue optional lt atom name gt Name of atom optional Context After all segments have been built and patched 37 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 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 reset Purpose Clears the structure topology definitions and aliases creating clean environment just like a new context Arguments Context At any time psfcontext create Purpose Creates a new context and returns its ID but does not switch
39. molly on is specified in which case the upper limit is perhaps doubled e nonbondedFreg lt timesteps between nonbonded evaluation gt Acceptable Values positive integer factor of fullElectFrequency 59 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 range nonbonded forces every 2 fs and long range electrostatics every 4 fs 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 longSplitting lt how should long and short range forces be split gt Acceptable Values xplor c1 Default Value c1 Description Specifies the method used to split electrostatic forces between long and short range potentials The xplor option uses the X PLOR shifting function and the c1 splitting uses the following C1 continuous shifting function 26 SW rij 0 if Fi gt Roff SW rij 1if Fiz lt Ron if Roff gt Fizl gt Ron where Ron is a constant defined using the configuration value switchdist Roz is specified using the configuration va
40. of mean force PMF calculation with this flag because the biasing forces would not be applied uniformly Also when disabling the forces on one of several groups defining a colvar a non zero net force or torque is applied to the entire system leading to an undesired center of mass motion resp rotation To minimize the length of the NAMD standard output messages from the previous options are not echoed by default They can be enabled by using the boolean keyword verboseOutput Recommendations for using atom groups Nearly all the calculations of colvar components are based on user specified atom groups These guidelines could be useful when choosing the atom groups to define a collective variable e When using periodic boundary conditions NAMD maintains the coordinates of all the atoms within a molecule contiguous to each other i e there are no jumps due to the periodic boundary conditions The colvar module relies on this when calculating a group s center of mass but this condition may fail when the group spans different molecules In this case writing the NAMD output files wrapA11 or wrapWater could produce wrong results when a simulation run is continued from a previous one There are however cases in which wrapA11 or wrapWater can be safely applied i the group has only one atom 105 ii it has all its atoms within the same molecule iii it is used by a colvar component which does not access its center of mass co
41. optimization cleardrops All available atoms will be iterated over by nextatom as if dropatom had never been called 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 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 getmass Returns the mass of the current atom getcharge Returns the charge of the current atom getid Returns the 1 based ID of the current atom addforce lt fx gt lt fy gt lt fz gt Adds the specified force to the current atom for this step 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 Are replicated in the following script 86 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 HH H proc calcforces step unique R K if step 20 0 4 cleardrops if unique print clearing dropped atom list at step step s
42. or no 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 limitdist lt maximum distance between pairs for limiting interaction strength A gt Acceptable Values non negative decimal Default Value 0 45 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 encouraged to experiment There should be no performance impact from enabling this feature 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 momen
43. the NAMD log output in most operating systems but it is synchronized with the disks every time the restart file is written e trajAppend lt global Append to trajectory file gt 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 92 e colvarsRestartFrequency lt global Colvar module restart frequency gt 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 analysis lt global Turn on analysis calculations gt Acceptable Values boolean Default Value off Description If this flag is enabled the analysis mode is turned on and all the colvars and biasing methods are instructed to perform whatever analysis they are configured to e readTrajectory lt global analysis mode Trajectory file to read gt Acceptable Values UNIX filename Description If analysis is on and the colvar module has been compiled as standalone the values of the colvars is read from this file as if a regular simulation was going on The same configuration as that of the run which produced the trajectory should be used to ensu
44. the calculation is one dimensional are written on disk at the given time interval e inputPrefix lt ABF Filename prefix for reading ABF data gt 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 ABF Apply the ABF bias gt 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 intended for testing purposes and should not be used in routine simulations ABF also depends on parameters from collective variables to define the grid on which free energy
45. the correlation function gt 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 which must be of the same type scalar vector or quaternion of amp e corrFuncType lt colvar Type of the correlation function gt Acceptable Values velocity coordinate or coordinate p2 Default Value velocity Description With coordinate or velocity the correlation function Cj t O amp to Ej to t is calculated between the variables and or their velocities O 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 3cos 9 1 2 is used instead of the cosine e corrFuncNormalize lt colvar Normalize the time correlation function gt Acceptable Values boolean 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 106 e corrFuncLength lt colvar Length of the time correlation function gt Acceptable Values positive integer Default Value 1000 Description Length in number of points of the time correlation function e corrFuncStride lt colvar Stride of the tim
46. the ensembles representative of states a and b are too disparate equation 29 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 T 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 elecLambdaStart or vdwLambdaEnd Sample TI data log ay 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 eo 4 Aas EAN e aca 10 76 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
47. 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 applied 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 i
48. tiElecLambdaStart At A 0 electrostatic interactions are fully coupled to the simulation and then linearly decreased with increasing such that at A values greater than or equal to 1 0 fepElecLambdaStart tiElecLambdaStart electrostatic interactions are completely decoupled from the simulation Two examples shown in Figure 10 describe the relationship between the user defined value of A and the coupling of electrostatic or vdW interactions to the simulation e fepVdwLambdaEnd tiVdwLambdaEnd lt Value of to cancel van der Waals interactions gt Acceptable Values positive decimal Default Value 1 0 Description Ifthe above fepElecLambdaStart tiElecLambdaStart option is being used it may be further desirable to separate the scaling of van der Waals and electrostatic interac 122 tions fepVdwLambdaEnd tiVdwLambdaEnd sets the value of A above which all vdW interac tions 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 greater than or equal to fepVdwLambdaEnd tiVdwLambdaEnd the vdW interactions of the exnihilated particle are fully coupled to the simulation For an annihilated particle vdW interactions are completely coupled to the simu lation at A 0 This coupling linearly decreases for A values between 1 0 and 1 fepVdwLambdaEnd tiVdwL
49. 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 and working backwards in can also som
50. 1 0e 4 Description Varying this might improve conjugate gradient performance 6 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 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 6 3 Dynamics 6 3 1 Timestep parameters e numsteps lt number of timesteps gt Acceptable Values positive integer 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 57 Default Value 1 0 Description The timestep size to use when integrating each step of the simulation T
51. 2 binaries for these platforms can also be run directly known as standalone mode for single process runs 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 Since 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 15 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 For multicore workstations Windows and Mac OX X Intel released binaries are based on multicore 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 The Solaris Sparc and x86 64 released binaries are based on smp builds of Charm that can be used with multiple threads on either a
52. 6 34 28 29 for the description of chemical changes in the molecular systems between the reference and the target states 10 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 20 36 2 The hybrid Hamiltonian of the system 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 27 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 t
53. AMD 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 simulation in order to exclude startup costs and allow for initial load balancing We provide both standard UDP and TCP based precompiled binaries for Linux clusters We have observed that the TCP version is better on our dual processor clusters with gigabit ethernet while the basic UDP version is superior on our single processor fast ethernet cluster When using the UDP version with gigabit you can add the giga option to adjust several tuning parameters Additional performance may be gained b
54. ARMM 8 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 11 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 e Force Field Compatibility The force field used by NAMD is the same as that used by the programs CHARMM 8 and X PLOR 9 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 forces 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
55. 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 66 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 LangevinPistonTemp lt noise temperature K gt Acceptable Values positive decimal Description Specifies barostat noise temperature for Langevin piston method Thi
56. D configuration the name of this file can be provided as colvarsInput to continue the simulation in the next run e if either colvarsRestartFrequency or the NAMD parameter restartFreq is defined a restart file equivalent to the state file is written every colvarsRestartFrequency steps named lt restartName gt colvars state the name of this file can be provided as colvarsInput to continue an interrupted run provided that the corresponding restart files for coordinates and velocities are used e if the colvars module parameter colvarsTrajFrequency is greater than 0 default 1 a trajectory file is written during the simulation with the name lt outputName gt colvars traj it is not needed to restart a simulation but it can be read in for post processing see 9 2 4 Other output files can written by specific methods applied to the colvars e g by the ABF method see 9 3 1 or the metadynamics method see 9 3 2 as for the colvar trajectory file they are meant for analyzing rather than continuing a simulation All such files begin with the prefix lt outputName gt 9 1 3 Colvars module configuration file Figure 7 shows a typical collective variables configuration file Its syntax is similar to that of the NAMD configuration file 2 2 1 with a few differences e the sign between a keyword and its value deprecated in the NAMD config is not allowed in the colvars config i e only keyword value is valid and not
57. D 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 simulation 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 i
58. E OF THE SOFTWARE AND OR ASSOCIATED MATERIALS LICENSEE AGREES THAT UNIVERSITY SHALL NOT BE HELD LIABLE FOR ANY DI RECT INDIRECT CONSEQUENTIAL OR INCIDENTAL DAMAGES WITH RESPECT TO ANY CLAIM BY LICENSEE OR ANY THIRD PARTY ON ACCOUNT OF OR ARISING FROM THIS AGREEMENT OR USE OF THE SOFTWARE AND OR ASSOCIATED MATERIALS 4 Licensee understands the Software is proprietary to Illinois Licensee agrees to take all reasonable steps to insure that the Software is protected and secured from unauthorized disclosure use or release and will treat it with at least the same level of care as Licensee would use to protect and secure its own proprietary computer programs and or information but using no less than a reasonable standard of care Licensee agrees to provide the Software only to any other person or entity who has registered with Illinois If licensee is not registering as an individual but as an institution or corporation each member of the institution or corporation who has access to or uses Software must understand and agree to the terms of this license If Licensee becomes aware of any unauthorized licensing copying or use of the Software Licensee shall promptly 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 no
59. M User s Manual 9 3 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 They are not unfortunately transportable between big endian most workstations and little endian Intel architectures This same caveat applies to binary velocity and coordinate files The utility programs flipdcd and flipbinpdb are provided with the Linux Intel version to reformat these files The exact format of these files is very ugly but supported by a wide range of analysis and display programs 19 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 fi
60. MDfreq 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 Ifno 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 8 9 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 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 8 10 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 acti
61. PDB format Binary files preserve more accuracy between NAMD restarts than ASCII PDB files but the binary files are not guaran teed to be transportable between computer architectures The utility program flipbinpdb is provided with the Linux Intel version to reformat these files DCDfile lt coordinate trajectory output file gt Acceptable Values UNIX filename 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 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 DCDUnitCell lt write unit cell data to ded 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 Description The binary DCD velocity trajectory filename This file stores the trajectory of all atom velocities using
62. Today s molecular dynamics simulations involve a large number of degrees of freedom typically 10 000 1 000 000 and it is often useful to reduce the description to a few parameters which can be either analyzed individually or manipulated in order to alter the dynamics of the system in a controlled manner Such reduced degrees of freedom have been called order parameters collective variables surrogate reaction coordinates and many other terms In this section the term collective variable shortened to colvar is used and it indicates any differentiable function of atomic Cartesian coordinates with between 1 and N the total number of atoms E t wilt aj t alt LSt j k SN 11 The collective variables module in NAMD offers a mechanism to define several collective vari ables and execute various tasks on them Its most important features are e defining an arbitrary number of colvars and perform a multidimensional analysis or biased simulation by accessing any subset of colvars independently from the others see 9 1 e combine different functions of Cartesian coordinates herein termed colvar components into a colvar defined as a polynomial of several such components thereby implementing new func tional forms at runtime periodic multidimensional and symmetric components are handled transparently see 9 2 1 e calculate potentials of mean force PMFs or free energy surfaces for a
63. UHA ON 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 ee ee Graph showing a slice of a ramp potential showing the effect of mgridforcevoff Example of a collective variables colvar configuration The colvar d is defined as the difference between two distances each calculated between the centers of mass of two atom groups The second colvar c holds the coordination number i e the number of contacts within a radius of 6 A between two groups The third colvar alpha measures the degree of a helicity of the protein segment between residues 1 and 10 A moving harmonic restraint is applied to the colvars d and c each rescaled by means of width parameters wg and we the centers of the restraint do and co evolve with the simulation time t The histogram of alpha and c is also recorded On th sani pangoni enaa wea p ad hh eae ne Fe E cae al ae p A typical colvars configuration file 0 0 e 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 state ink tA eo et ak Be he i eae a a a ed Se GR eal Convergence of an FEP calculation If
64. 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 8 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 may be discontin uous in simulations using periodic boundary conditions if for example a charged hydrogen group moves outside of the central cell There are two 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 of decimals x y z Description Vector which describes the electric field to be applied Units are kcal mol A 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
65. 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 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 is 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 88 9 Collective Variable based Calculations The features described in this section were contributed by Giacomo Fiorin and J r me H nin Center for Molecular Modeling University of Pennsylvania The collective variables module replaces and greatly extends the functionality of the older freeEnergy module for free energy of conformational change calculations The older module is still available in the code but has been removed from the documentation to discourage future use
66. acting 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 features 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 t
67. al 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 TBG 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 uiuc 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 Biophysics Group Beckman Institute University of Illinois 405 North Mathews MC 251 Urbana Illinois 61801 USA FAX
68. ambdaEnd For A values greater than or equal to 1 fepVdwLambdaEnd tiVdwLambdaEnd vdW interactions of the annihilated particle are fully decoupled from the simulation e decouple decouple lt Disable scaling of nonbonded interactions within alchemical par titions gt Acceptable Values on or off Default Value off Description With decouple 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 decouple 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 informa tive 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 13 10 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 6A 0 1 fep On Turn FEP functionality on fepFile ion fep File containing the information about grow fepCol xX ing shrinking atoms described in column X fepOutfile i
69. and S C Harvey Dynamics of Proteins and Nucleic Acids Cambridge University Press Cambridge 1987 D A Pearlman A comparison of alternative approaches to free energy calculations J Phys Chem 98 1487 1493 1994 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 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 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 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 P
70. and nonbonded terms The bonded potential terms involve 2 3 and 4 body interactions of covalently bonded atoms 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 distan
71. aoa ee 5 1 1 Bonded potential energy terms e 5 1 2 Nonbonded potential energy terms aooo a 5 2 Non bonded interactions a e 5 2 1 Van der Waals interactions a 5 2 2 Electrostatic interactions a 5 2 3 Non bonded force field parameters a 5 2 4 PME parameters ia n ohne E E a a Sh o EnA ae o a 5 2 5 Full direct parameters osoo e 5 2 6 DPME parameters en woi a E a a a a e E Ea e a 11 11 13 13 15 15 15 15 16 18 19 19 19 19 19 19 20 20 21 23 24 26 28 28 29 29 30 34 35 40 5 27 DPMTA parameters s an ey ea a a eR ee Re 5 3 Constraints and Restraints e 5 3 1 Bond constraint parameters e 5 3 2 Harmonic restraint parameters e 5 3 3 Fixed atoms parameters Standard Minimization and Dynamics Parameters 6 1 Boundary Conditions ea e Som ok eee a a RS 6 1 1 Periodic boundary conditions 0 o 6 1 2 Spherical harmonic boundary conditions 2 6 1 3 Cylindrical harmonic boundary conditions 6 2 Energy Minimization a 6 2 1 Conjugate gradient parameters a a 6 2 2 Velocity quenching parameters 0 0000 e eee ee eee O 3 Dynamics sss ss Yet es Bee Be Hee A PO Ge a ee BOR A Ee eR ta 6 3 1 Timestep parameters 2 2 e 6 3 2 Tnitialization a t 5 es awl eck a RAO Ge 6 3 3 Conserving momentum 2 0 0000 ee ee ee 6 3 4
72. ar e upperBoundary lt colvar Upper boundary of the colvar gt Acceptable Values positive decimal Description Similarly to lowerBoundary defines the highest possible or allowed value e lowerWallConstant lt colvar Lower boundary force constant kcal mol gt Acceptable Values positive decimal 94 Description If lowerBoundary is defined enables a lower bounding restraint on the colvar in the form of a half harmonic potential centered on lowerBoundary The energy scale of the constant is kcal mol while the spatial scale is that of the colvar upperWallConstant lt colvar Upper boundary force constant kcal mol gt Acceptable Values positive decimal Description If upperBoundary is defined enables an upper bounding restraint on the colvar The unit is the same as lowerWallConstant outputValue lt colvar Output a trajectory for this colvar gt Acceptable Values boolean Default Value on Description If colvarsTrajFrequency is defined the value of this colvar are written to the trajectory file every colvarsTrajFrequency steps in the column labeled lt name gt outputVelocity lt colvar Output a velocity trajectory for this colvar gt 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 outputSystemForce lt colvar Ou
73. aries are available for download for the following platforms e Windows XP etc on x86 processors e Mac OS X on PowerPC and Intel processors e Linux on x86 x86 64 and Itanium processors e SGI Altix with MPI e AIX on POWER processors with and without MPI e Solaris on Sparc and x86 64 processors NAMD has been ported to the Cray XT for both Catamount and compute node Linux but the lack of dynamic linking on this platform often results in the need to recompile NAMD after system upgrades so we are unable to distribute useful binaries NAMD has been ported to the IBM Blue Gene L and P but we do not have regular access to these machines Binaries provided by IBM may be available for download from our website 16 3 Compiling NAMD We provide complete and optimized binaries for all platforms to which NAMD has been ported It should not be necessary for you to compile NAMD unless you wish to add or modify features or to improve performance by using 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 16 4 Documentation All available NAMD documentation is available for download without registration via the NAMD web site http www ks uiuc edu Research namd 148 References 1 10 11 12 13 14 15
74. ase all of the ATOM records are read or ii a larger number of atoms in which case atoms will be selected according to refPositionsCol A typical usage may be to reuse atomsFile Unlike atomsFile however it need not match the number of atoms in the topology e refPositionsCol lt atom group Reference positions for the group gt Acceptable Values X Y Z 0 or B Default Value 0 Description Analogous to atomsCol e refPositionsColValue lt atom group Value in the PDB column gt Acceptable Values positive decimal Description Analogous to atomsColValue e refPositionsGroup lt atom group Group to be used gt Acceptable Values Block refPositionsGroup Default Value This group itself Description If either centerReference or rotateReference is defined this keyword allows to define an additional atom group which is used instead of this one to calculate the translation or the rotation to the reference positions e disableForces lt atom group Disable application of colvar forces on this group gt Acceptable Values boolean Default Value off Description If this option is on all the forces applied from the colvars to the atoms in this group are ignored However the applied forces on each colvar are still written to the trajectory file if requested In some cases it may be desirable to use this option in order not to perturb the motion of selected groups of atoms However it is not advisable to perform a potential
75. ationAngle accepts the same options of rmsd and orientation atoms refPositions refPositionsFile and refPositionsCol but it returns instead the angle of rotation 0 between the current and the reference positions This angle is expressed in degrees within the range 180 180 Component gyration radius of gyration The block gyration defines the parameters for calculating the radius of gyration of a group of atomic positions x1 t x2 t xn t with 100 respect to their center of geometry Xcog t ee 5 Raye 4 F Y lt Xoglt 15 4 1 This component must contain one atoms block to define the atom group and returns a positive number expressed in A Component 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 No Q No No1 G No 1 No 5 No 5 GQ Not 5 No tN C No N al 0 0 CS O oN Cy O yoo N Cy 16 1 No N 2 1 No N 4 PASS n 2 ER hbf OM N 4 2 N 2 ze angf ch Cy Cy 2 N 4 2 o 17 where the score function for the Cg Ca Ca angle is defined as 2 1 008 cL CH 80 Abo angf C CD oga 18 4 1 arc n CD pta _ 00 J Abi and the score function for the O Y N 4 hydrogen bond is defined through a hBo
76. ault Value 2 Description Exponent for second boundary potential The only likely values to use are 2 and 4 6 2 Energy Minimization 6 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 is used to select successive search directions starting with the initial gradient which eliminate repeated 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 56 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
77. 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 x Berendsen pressure coupling 12 Nos Hoover Langevin piston Energy minimization Fixed atoms 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 1t is designed in an object oriented style with C Since molecular dynam ics 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 contem plating a particular modification to NAMD you are encouraged to contact the developers at namd ks uiuc edu for guidance e Interactive MD simulations A system undergoing simulation 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 spatia
78. before pdb is called Arguments lt file name gt PDB file containing known or aliased residues Context Anywhere within segment 36 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 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 built 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
79. bond stretch valence angle deformation and torsions in the course of the simulation 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 7 This property is controlled by the decouple keyword described in 10 1 2 Free Energy Perturbation Within the FEP framework 6 12 13 21 30 34 43 44 46 the free energy difference between two alternate states a and b is expressed by 118 AA In exp 8 Ho x Pr Hal Pa a 29 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 representative of the initial reference state a a e X a X b X c Figure 9 Convergence of an FEP calculation If the ensembles representative of states a and b are too disparate equation 29 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 refle
80. ce between the pair of atoms and rup is the equilibrium distance The 4 body torsion angle also known as dihedral 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 Al 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
81. ce with pdb May call multiple times e 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 35 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 commands 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 f
82. ch 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 clearconfig Clears the current list of requested atoms After clearconfig calls to addatom and addgroup can be used to build a new configuration getstep Returns the current step number 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 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 loadtotalforces lt varname gt Loads the total forces on each requested atom in the previous time step in kcal mol A7 into a local array The total force also includes external forces Note that the 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 loadmasses lt varname gt Loads requested atom and group masses
83. ch 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 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 54 e sphericalBCexp1 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 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 6 1 3 Cylindrical harmonic boundary conditions NAMD provides cylindrical
84. chdist lt distance at which to activate switching splitting function for electrostatic 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 44 see Section 5 2 exclude lt 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 connected 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 ar
85. cient exploration of reactive potential energy surfaces using car parrinello molecular dynamics Phys Rev Lett 90 23 238302 2003 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 mechanics 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 A Laio and M Parrinello Escaping free energy minima Proc Natl Acad Sci USA 99 20 12562 12566 2002 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 150 34 35 36 37 42 43 44 45 46 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 Encyclopedia of computational chemistry volume 2 pages 1070 1083 Wiley and Sons Chichester 1998 J A McCammon
86. cted 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 Px is assumed to be identical for state a and state b Convergence of equation 29 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 9 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 6 28 29 34 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 30 i 1 Here N stands for the number of intermediate stages or windows between the initial and the final states see Figure 9 10 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 29 42 19 aa UE ay 31 In the multi configuration thermodynamic integration approach 42 implemented in NAMD OH x Px A OA the ensemble average of the derivative of the internal energy with respect to A
87. ctor field see equation 23 in section 9 3 1 that only involves atoms of group1 This option is only useful for ABF or custom biases that compute system forces See section 9 3 1 for details The value returned is a positive number in A limited between 0 and the largest possible inter atomic distance within the chosen boundary conditions in PBC the minimum image convention is used Component distanceZ projection of a distance on an axis The distanceZ block defines a distance projection component which can be seen as measuring the distance 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 e main lt distanceZ distanceXY Main group of atoms gt Acceptable Values Block main Description Group of atoms whose position r is measured e ref lt distanceZ distanceXY Reference group of atoms gt Acceptable Values Block ref Description Reference group of atoms The position of its center of mass is noted r below 96 e ref2 lt distanceZ distanceXY Secondary reference group gt Acceptable Values Block ref2 Default Value none Description Optional group of reference atoms whose position r2 can be used to define a dynamic projection axis e r2 r1 1 7 x ra r In this case the origin is rm 1 2 r1 r2 and the
88. d in the DPMTA calculation The default value is based on recommendations by the developers of the code e FMAFFTBlock lt blocking factor for FMA FFT gt Acceptable Values positive integer Default Value 4 Description The blocking factor for the FFT enhancement to DPMTA This parameter is only used if both FMA and FMAFFT are set to on The default value of 4 should be suitable for most applications 5 3 Constraints and Restraints 5 3 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 algorithm 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 Sha
89. d in the score function 18 e hBondCutoff lt alpha Hydrogen bond cutoff gt Acceptable Values positive decimal Default Value 3 3 A Description Equivalent to the cutoff option in the hBond component e hBondExpNumer lt alpha Hydrogen bond numerator exponent gt Acceptable Values positive integer Default Value 6 Description Equivalent to the expNumer option in the hBond component e hBondExpDenom lt alpha Hydrogen bond denominator exponent gt 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 9 2 2 Linear and polynomial combinations of components 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 12 can be obtained by setting the following parameters which are common to all components e componentExp lt any component Exponent of this component in the colvar gt 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 no
90. d 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 The following parameters describe the grid based potentials e 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 e 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 e 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 e mgridforceqcol lt 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 c
91. ded 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 67 7 Performance Tuning 7 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 A Consider a pair of atoms A and B that are 8 1 A apart when the pairlist is built If the pair list includes
92. describes how options are specified within a NAMD configuration file Section 2 2 3 lists the parameters which are required to run a basic simulation Section 13 describes the relation between specific NAMD and X PLOR dynamics options Several sample NAMD configuration files are shown in section 14 2 2 1 Configuration parameter syntax Each line 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 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 15 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
93. e 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 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 PDB file gt Acceptable Values UNIX filename prefix Description At the end of every simulation NAMD writes two PDB 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 The position coordinates will be saved to a file named as this prefix with coor 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 e binaryoutput lt use binary output files gt Acceptable Values yes or no Default Value yes Description Activates the use of binary output files If this option is set to yes then the final output files will be written in binary rather than PDB format Binary files preserve more accuracy between NAMD restar
94. e 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 Currently the only available method is the impulse based Verlet 1 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 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
95. e X PLOR format names for atom types the default 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 Purpose Read in structure information from PSF file and adds it to the structure 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 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 from 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 Coo
96. e axis The axis is defined using the axis parameter or as the vector joining ref and ref2 see distanceZ above Component distanceVec distance vector between two groups The distanceVec block defines a distance vector component which accepts the same options as distance group1 and group2 It returns a 3 dimensional vector d dz dy dz The range of values of dz dy and d in A is determined by the chosen boundary conditions Component distanceDir distance unit vector between two groups The distanceDir block defines a distance unit vector component which accepts the same op tions as distance group1 and group2 It returns a 3 dimensional unit vector d dz dy dz d 1 dz dy and d lie within the 1 1 interval Component angle angle between three groups The angle block defines an angle which accepts the options group1 group2 and group3 to define the three groups It returns an angle in degrees within the interval 0 180 97 Component dihedral torsional angle between four groups The dihedral block defines a torsional angle which accepts the options group1 group2 group3 and group4 to define 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
97. e case sensitive string which 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 Typical fluctuation amplitude or grid spacing gt Acceptable Values positive decimal Default Value 1 0 Description This number is a user provided estimate of the typical fluctuation amplitude for this collective variable or conversely the typical width of a local free energy basin Typi cally twice the standard deviation of this variable during a short simulation run can be used Biasing methods use this parameter for different purposes harmonic restraints 9 3 3 use it to rescale the value of this colvar ABF 9 3 1 interprets it as the grid spacing in the direction of this variable and metadynamics 9 3 2 uses it as the width of newly added gaussians This number is expressed in the same physical unit as the colvar value e lowerBoundary lt colvar Lower boundary of the colvar gt Acceptable Values positive decimal Description Defines the lowest possible value of this colvar that should be sampled in the simulation It can either be a true physical boundary under which the variable is not defined by construction or an artificially imposed repulsive wall if lowerWallConstant is also defined Together with upperBoundary and width it defines a grid of values for the colvar This number can only be defined for a scalar colv
98. e correlation function gt Acceptable Values positive integer Default Value 1 Description Number of steps between two values of the time correlation function e corrFuncOffset lt colvar Offset of the time correlation function gt Acceptable Values positive integer Default Value 0 Description The starting 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 e corrFuncOutputFile lt colvar Output file for the time correlation function gt Acceptable Values UNIX filename Default Value lt name gt corrfunc dat Description The time correlation function is saved in this file e runAve lt colvar Calculate the running average and standard deviation gt Acceptable Values boolean Default Value off Description Whether or not the running average and standard deviation should be cal culated for this colvar e runAveLength lt colvar Length of the running average window gt Acceptable Values positive integer Default Value 1000 Description Length in number of points of the running average window e runAveStride lt colvar Stride of the running average window values gt Acceptable Values positive integer Default Value 1 Description Number of steps between two values within the running average window e runAve0utputFile lt colvar Output file for the running average and standard deviation gt Acceptable Values UNIX fil
99. e 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 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 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 1 4scaling lt scaling factor for 1 4 interactions gt Acceptable Values 0 lt decimal lt 1 Default Value 1 0 Description Scaling factor for 1 4 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 inter actions 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 vdwGeometricSigma lt use geometric mean to combine L J sigmas gt Acceptable Values yes
100. e file e FFTWWisdomFile lt name of file for FFTW wisdom archive gt Acceptable Values file name Default Value FFTW_NAMD_version_platform txt 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 likely sufficient as it is version and platform specific 5 2 5 Full direct parameters The direct 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 DPMTA or PME to compute full electrostatics 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 47 5 2 6 DPME parameters DPME is an implementation of PME that is no longer included in the released NAMD binaries We recommend that you use the current PME implementation e useDPME lt Use old DPME code gt Acceptable Values yes or no Default Value no Description Switches to old DPME implementation of particle mesh Ewald The new code is faster and allows non orthogonal cells so you probably just want to leave t
101. e 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 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 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 2 5 2 U 7 7 t sh ot R t Ry a 10 Here t Nisdt where Ni 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 Out
102. e 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 NAMD 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 12 1 for details as well as the example scripts in Sec 14 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 th
103. e or tiFile 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 125 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 elec vdW Subtotal 222 o io io is Part 1 0 5748 6 3452 6 9200 Part 2 0 5391 4 9387 5 4778 7227 O EEn Subtotal 0 6048 0 3293 12 3978 Total deltaG for transition lambda 0 gt 1 12 3978 may encourage interpretations along the lines of the free energy for switching on the van der Waals interactions for the atoms of partition 1 was 6 35kcal mol This is only correct in the very narrow context of the simulation setup and parameters used in this case and is not informative in a broader sense The choice of A 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 particular it will be neces
104. e to thank the members of the Theoretical Biophysics Group past and present who have helped tremendously in making suggestions pushing for new features and testing bug ridden code 14 2 Getting Started 2 1 What is needed Before running NAMD explained in section 15 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 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 should continue etc Section 2 2 1
105. eConstantArea useConstantRatio LangevinPis ton LangevinPiston Target LangevinPistonPeriod LangevinPistonDecay LangevinPiston Temp Surface Tension Target BerendsenPressure BerendsenPressureTarget BerendsenPres sureCompressibility and BerendsenPressureRelaxation Time parameters may be changed to 16 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 e The checkpoint and revert commands no arguments allow a scripted simulation to save and restore to a prior state 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 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 modul
106. ed in the group atomsColValue lt atom group Value in the PDB column gt Acceptable Values positive decimal Description If defined this value identifies in atomsCol of atomsFile which atoms are to be read otherwise all atoms with a non zero value will be read dummyAtom lt atom group Dummy atom position A gt Acceptable Values x y z triplet Description If no actual atoms are defined for the group this option may be used to make this group return a fixed position in space This is useful e g to make colvar components that normally calculate functions of the group s center of mass work with an absolute reference position If this option is specified for the group disableForces is turned on the x y z position provided is returned as its center of mass and zero velocities and system forces are reported centerReference lt atom group Ignore the translations of this group gt Acceptable Values boolean Default Value off Description If this option is on the center of mass of this group is centered on a refer ence frame determined either by refPositions or refPositionsFile This transformation occurs before any colvar component has access to the coordinates of the group hence only the recentered coordinates are available to the colvars rotateReference lt atom group Ignore the rotations of this group gt Acceptable Values boolean Default Value off Description If this option is on this group
107. ed parameter 58 segment psfgen command 35 selectConstraints parameter 51 selectConstrX parameter 51 selectConstrY parameter 51 selectConstrZ parameter 51 MD parameter 80 MDDir parameter 80 MDFile parameter 80 MDk parameter 80 MDOutputFreq parameter 80 MDVel parameter 80 source command 16 sphericalBC parameter 54 sphericalBCCenter parameter 54 sphericalBCexp1 parameter 55 sphericalBCexp2 parameter 55 sphericalBCk1 parameter 54 sphericalBCk2 parameter 55 sphericalBCr1 parameter 54 S S S S S S sphericalBCr2 parameter 55 splitPatch parameter 70 stepspercycle parameter 70 StrainRate parameter 67 structure parameter 20 Surface TensionTarget parameter 67 switchdist parameter 44 switching parameter 44 targets parameter 115 targetsNumSteps parameter 116 tclBC parameter 85 tclBCArgs parameter 85 tclBCScript parameter 85 tclForces parameter 81 tclForcesScript parameter 81 tCouple parameter 62 tCoupleCol parameter 62 tCoupleFile parameter 62 tCoupleTemp parameter 62 TEMPAVG 23 temperature parameter 58 timestep parameter 57 MD parameter 78 MDFile parameter 78 MDFinalRMSD parameter 79 MDFirstStep parameter 78 MDInitialRMSD parameter 79 MDk parameter 78 MDLastStep parameter 78 MDOutputFreq parameter 78 topology psfgen command 35 TOTAL2 energy 23 TOTALS energy 23 trajAppend parameter 92 twoAwayX 147 twoAwayY 147 twoAwayZ 147 T T T T T T T T
108. eee ee ee 10 4 2 Thermodynamic Integration 2 0 000002 eee eee 11 Accelerated Sampling Methods 11 1 Locally enhanced sampling Tiir Striictire generation i sop maosa r Pt we ee Ee are SR a ee Be 11 1 2 Simulation a whee en feed hak eens Ge ewe ek genes yoko 11 2 Replica exchange simulations e 12 Runtime Analysis 12 1 Pair interaction calculations ooa ee 12 2 Pressure profile calculations ee 13 Translation between NAMD and X PLOR configuration parameters 14 Sample configuration files 15 Running NAMD 15 1 Individual Windows Linux Mac OS X or Other Unix Workstations 15 2 Linux or Other Unix Workstation Networks 0 0 000202 005 15 3 Windows Workstation Networks o 0000 o ASGAR ont ts eA a Oe heh ei Ne ER Ee he eS ee G 15 5 IBM POWER Clusters aaa 15 6 Memory Usage cose 2 oS eg eo A sede bY Ate we de ee 89 89 90 91 91 93 96 102 102 106 107 108 112 115 116 117 117 117 118 119 120 123 125 125 125 128 128 128 128 129 132 132 133 137 139 15 7 Improving Parallel Scaling e 16 NAMD Availability and Installation 16 1 How to obtain NAMD 3 5 2 82434 a a ee a ee 16 2 Platforms on which NAMD will currently run o e o 16 3Complliine NAMI p ieg aaee 4 RI de PMO a a SE a Be 16 4 Documentation References Index 148 148 148 148 148 149 152 List of Figures O 0
109. ename Default Value lt name gt runave dat Description The running average and standard deviation are saved in this file 9 3 Biasing and analysis methods All of the biasing and analysis methods implemented recognize the following options e name lt colvar bias Identifier for the bias gt Acceptable Values string Default Value lt type of bias gt lt bias index gt 107 Description This string is used to identify the bias or analysis method in output messages and to name some output files e colvars lt colvar bias Collective variables involved gt 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 9 3 1 Adaptive Biasing Force calculations For a full description of the Adaptive Biasing Force method see reference 17 For details about this implementation see reference 23 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 Eielt n is defined from the canonical distribution of P amp A 7 In P E Ao 19 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 Fe 20 Several formulae that take the form of 20 have been proposed This
110. er1 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 requires 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 30 pdb output 6PTI_protein pdb 5 Patch protei
111. erates 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 XSTfile lt XST file to write cell trajectory to gt Acceptable Values file name Description _NAMD can also generate a xst eXtended System Trajectory file which contains a record of the periodic cell parameters and extended system variables during the simulation If XSTfile is defined then XSTfreq must also be defined XSTfreq lt how often to append state to XST file gt Acceptable Values positive integer Description Like the DCDfreq option controls how often the extended system configura tion will be appended to the XST file 53 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 c
112. es 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 column indicates that the atom is not enhanced Any other value should be a positive integer less than lesFactor 11 2 Replica exchange simulations The 1ib replica directory contains Tcl scripts that implement replica exchange for NAMD using a Tcl server and socket connections to drive a separate NAMD process for every replica used in the simulation Replica exchanges and energies are recorded in the potenergy dat realtemp dat and targtemp dat files written in the output directory These can be viewed with e g xmgrace nxy potenergy dat There is also a script to load the output into VMD and color each frame according to target temperature An example simulation folds a 66 atom model of a deca alanine helix in about 10 ns This implementation is designed to be modified by the user to implement exchanges of pa rameters other than temperature or via ot
113. es 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 137 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 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
114. escription SMD harmonic constraint force constant Must be specified in kcal mol A The conversion factor is 1 kcal mol 69 479 pN A e 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 e 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 e SMDOutputFreq 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 8 8 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 view the current state of the system or perform interactive steering 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 80 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 I
115. et R expr 1 R set R2 expr R R set tol 2 0 set cut2 expr R tol R tol while nextatom 4 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 8 11 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 87 extForces lt Apply external program forces gt Acceptable Values yes or no Default Value no Description Specifies whether or not external program forces are applied 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 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
116. etimes 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 69 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 When set to hydrogen hydrogen at
117. 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 20 140 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 32 141 This file demonstrates the 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 12 1 for more about pair interaction calculations initial config coordinates alanin pdb temperature 0 output params outputname tmp alanin analyze binaryoutput no integra
118. f 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 be reduced to correspond with the 128 reduced potential This option affects velocity initialization reinititialization reassignment and the target temperature for langevin dynamics Langevin dynamics is recommended with 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 Valu
119. fcontext reset psfgen command 38 psfcontext stats psfgen command 38 psfSegID parameter 101 103 readBegin parameter 93 readEnd parameter 93 readexclusions parameter 24 readpsf psfgen command 39 read Trajectory parameter 93 reassignFreq parameter 63 reassignHold parameter 63 reassignIncr parameter 63 reassign Temp parameter 63 ref parameter 96 ref2 parameter 97 refPositions parameter 99 104 refPositionsCol parameter 100 105 refPositionsColValue parameter 100 105 refPositionsFile parameter 100 104 refPositionsGroup parameter 105 regenerate psfgen command 37 reinitvels command 17 reloadCharges command 17 replica exchange 129 replicaFilesRegistry parameter 114 replicalD parameter 114 155 replicaUpdateFrequency parameter 115 rescaleFreq parameter 62 rescale Temp parameter 62 rescalevels command 17 resetpsf psfgen command 38 residue psfgen command 36 residueRange parameter 101 restartfreq parameter 22 restartname parameter 21 restartsave parameter 22 rigidBonds parameter 49 rigidDieOnError parameter 50 rigidIterations parameter 49 rigidTolerance parameter 49 rotateReference parameter 104 rotConsAxis parameter 77 rotConsPivot parameter 77 rotConstraints parameter 77 rotConsVel parameter 77 run command 16 runAve parameter 107 runAveLength parameter 107 runAveOutputFile parameter 107 runAveStride parameter 107 saveFreeEnergyFile parameter 114 scnb parameter 24 se
120. fectively 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 Description Should moving restraints be applied to the system If set to on then movingConsVel must be defined May not be used with rotConstraints e movingConsVel lt Velocity of the reference position movement gt Acceptable Values vector in A timestep Description The velocity of the reference position movement Gives both absolute value and direction 8 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 76 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
121. files which not stored in the standard records of PSF files These informations are also available after a PSF file was read by command readpsf Here a a simple axample PSF REMARKS REMARKS REMARKS REMARKS REMARKS REMARKS REMARKS REMARKS REMARKS REMARKS 1704 INTITLE original generated structure x plor psf file 4 patches were applied to the molecule topology 1LOV_autopsf temp top segment P1 first NTER last CTER auto angles dihedrals segment 01 first NONE last NONE auto none segment W1 first NONE last NONE auto none defaultpatch NTER P1 1 defaultpatch CTER P1 104 patch DISU P1 10 P1 2 patch DISU P1 103 P1 6 NATOM 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 40 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
122. g commands manually 31 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 names 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
123. g temperature for equilibration K gt Acceptable Values positive decimal Description The final temperature for reassignment when reassignIncr is set reassignTemp will be held at this value once it has been reached This parameter is valid only if reassignIncr has been set 6 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 V3 where 8 is the compressibility which i
124. g the TI derivatives dumped every fepOutFreq tiOutFreq steps fepVdwShiftCoeff tiVdwShiftCoeff lt Soft core van der Waals radius shifting coeffi cient gt Acceptable Values positive decimal Default Value 5 Description This is a radius shifting coefficient of A that is used to construct the modi fied vdW interactions during alchemical free energy calculations Providing a positive value for fepVdWShiftCoeff tiVdwShiftCoeff ensures that the vdW potential is finite every where 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 simula tion 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 5 33 r r fepVdWShiftCoeff x 1 A fepElecLambdaStart tiElecLambdaStart lt Value of A to introduce electrostatic inter actions 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 5 13 One possible route for avoiding overlap of unbounded electrostatic poten tials consists of allowing a bounded soft core vdW potential
125. 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 water 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 ident
126. 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 lists standard minimization and dynamics parameters Section 7 lists performance tuning parameters Section 8 explains user defined forces conformation change calculations Section 9 describes collective variable based calculations Section 10 explains alchemical free energy calculations Section 11 presents accelerated sampling methods Section 12 lists runtime analysis options Section 13 provides hints for X PLOR users Section 14 provides sample configuration files Section 15 gives details on running NAMD Section 16 gives details on installing NAMD We have attempted to make this document complete and easy to understand and to make NAMD itself easy to install and run We welcome your suggestions for improving the documentation or code at namd ks uiuc edu 1 1 NAMD and molecular dynamics simulations Molecular 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 35 In order to conduct MD simulations various computer programs have been developed including X PLOR 9 and CH
127. gonality condition e and are based on non overlapping sets of atoms e 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 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 23 are mutually orthogonal The cases described for colvars in the previous paragraph apply 5 Orthogonality of colvars and constraints equation 22 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 constraint 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 22 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 Parameters for ABF The following parameters can be set in the ABF configuration block in addition to generic bias parameters such as colvars e fullSamples lt ABF Number
128. 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 coor1 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 17 r3 73 in radian This command takes the coordinates of the three atoms as input and returns a list of 1 ie oe Each element of the list is 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 72 73 74 in radian This command takes the coordinates of the four atoms as input and returns a list of Ea E oe oe Each element of the list is a 3 D vector in the form of a Tcl list 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 The IDs of the four atoms defining the dihedra
129. h to easily contain our protein resetpsf readpsf psffile readpsf watpsf coordpdb pdbfile coordpdb 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 of 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 34 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 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
130. h 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 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 equivalenc
131. h atom positions are to be read Otherwise all positions with a non zero value will be read This component returns a positive real number in A Component orientation orientation with respect to a reference structure The block orientation returns the same optimal rotation used in the rmsd component to superimpose the coordinates x t onto a set of reference coordinates xe It accepts all the options of rmsd atoms refPositions refPositionsFile and refPositionsCol and returns a four dimensional vector q qo 91 92 93 with gt gt q 1 this quaternion expresses the optimal rotation x t gt xe according to the formalism in reference 15 The quaternion qo q1 42 93 can also be written as cos 2 sin 2 u where is the angle and u the normalized axis of rotation for example a rotation of 90 around the z axis should be 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 matrix in a format suitable for usage in VMD Hint to restrain the rotation of a macromolecule in solution e g when one of the cell di mensions is much longer than the others it is possible to define a colvar with an orientation component and restrain it throuh the harmonic bias around the zero rotation 1 0 0 0 0 0 0 0 Component orientationAngle angle of rotation with respect to a reference structure The block orient
132. harge of the atom will be the product of the two values e mgridforcevfile lt tag gt lt grid potential file name gt Acceptable Values UNIX file name Description File specifying the grid size coordinates and potential values e mgridforcevolts lt tag gt lt grid potential units in eV 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 e e mgridforcescale lt tag gt lt scale factor for grid potential gt Acceptable Values decimal Description Scale factor applied to the grid potential values 74 e mgridforceconti lt tag gt lt Is grid continuous in the direction of the first basis vector gt Acceptable Values yes or no 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 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 t
133. 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 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 3 3 Fixed atoms parameters Atoms may be held fixed during a simulation NAMD avoids calculating most
134. hat 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 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 24 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 configu
135. he 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 6 3 2 Initialization e temperature lt initial temperature K gt Acceptable Values 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
136. he 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 Reading coordinates from the PDB files 28 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 m
137. he grid e mgridforcecont2 lt tag gt lt Is grid continuous in the direction of the second basis vector 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 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 the grid is defined for points 0 N 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 8 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 rt Fo Ut 8 A velocity vector Y movingConsVel needs to be specified The way the moving constraints wo
138. her temperature exchange methods The scripts should provide a good starting point for any simulation method requiring a number of loosely interacting systems replica_exchange tcl is the master Tcl script for replica exchange simulations it is run in tclsh outside of NAMD and takes a replica exchange config file as an argument tclsh replica_exchange tcl fold_alanin conf tclsh replica_exchange tcl restart_1 conf 129 replica_exchange tcl uses code in namd_replica_server tcl a general script for driving NAMD slaves and spawn_namd tcl a variety of methods for launching NAMD slaves 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 al1 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 A replica exchange config file should define the following Tcl variables num_replicas the number of replica simulations to use min_temp the lowest replica target temperature max_temp the highest replica target temperature steps_per_run the number of steps between exchange attempts num_runs the number of runs before stopping should be divisible by runs_per_frame x frames per restart
139. his option turned off If you set cell0rigin to something other than 0 0 0 the energy may differ slightly between the old and new implementations DPME is no longer included in released binaries 5 2 7 DPMTA parameters DPMTA is no longer included in the released NAMD binaries We recommend that you instead use PME with a periodic system because it conserves energy better is more efficient and is better parallelized If you must have the fast multipole algorithm you may compile NAMD yourself These parameters control the options to DPMTA an algorithm used to provide full electrostatic interactions DPMTA is a modified version of the FMA Fast Multipole Algorithm and unfortu nately most of the parameters still refer to FMA rather than DPMTA for historical reasons Don t be confused For a further description of how exactly full electrostatics are incorporated into NAMD see Section 6 3 4 For a greater level of detail about DPMTA and the specific meaning of its options see the DPMTA distribution which is available via anonymous FTP from the site ftp ee duke edu in the directory pub SciComp src e FMA lt use full electrostatics gt Acceptable Values on or off Default Value off Description Specifies whether or not the DPMTA algorithm from Duke University should be used to compute the full electrostatic interactions If set to on DPMTA will be used with a multiple timestep integration scheme to provide full electrostatic interacti
140. hys Chem 43 407 435 1992 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 biomolecular systems Theoretical and experimental applications pages 27 59 Escom The Netherlands 1989 A F Voter Hyperdynamics Accelerated molecular dynamics of infrequent events Phys Rev Lett 78 20 3908 3911 May 1997 R W Zwanzig High temperature equation of state by a perturbation method i nonpolar gases J Chem Phys 22 1420 1426 1954 151 Index 1 4scaling parameter 45 alias psfgen command 35 39 amber parameter 24 ambercoor parameter 24 analysis parameter 93 angleRef parameter 101 angle Tol parameter 102 applyBias parameter 110 atomNameResidueRange parameter 103 atomNumbers parameter 103 atomNumbersRange parameter 103 Atoms moving too fast 69 atoms parameter 99 atomsCol parameter 103 atomsColValue parameter 104 atomsFile parameter 103 auto psfgen command 36 axis parameter 97 Bad global exclusion count 69 BerendsenPressure parameter 65 BerendsenPressureCompressibility parame ter 65 BerendsenPressureFreq parameter 65 BerendsenPressureRelaxation Time ter 65 BerendsenPressureTarget parameter 65 binaryoutput parameter 21 binaryrestart parameter 22 bincoordinates parameter 21 binvelocities parameter 21 BOUNDARY energy 23 parame callback command
141. ical 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 32 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 33 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 enoug
142. icient 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 coefficients 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 6 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 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 62 6 4 4 Temperature reassignment parameters
143. imulation Whereas the FEP module of NAMD supplies free energy differences determined from equa tion 29 the wealth of information available in fepOutFile 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 32 Within the SOS framework the free energy difference between states A and A 41 is expressed as exp E Map Hs anit exp 4 24 x Pes Mi HS Pes Mis E e and can be readily used with the statistical information provided by the forward and the backward runs exp fAAz 441i l 32 10 4 2 Thermodynamic Integration When running TI free energy calculations the elec dU dl and vdW_dU dl values reported in ti0utFile are the derivatives of the internal energy with respect to A i e ze 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 ap pearing and the disappearing atoms are accounted for separately Partition 1 contains those atoms whose interactions are switched up as A increases i e flagged with 1 in the fepFil
144. ing for the electrostatic interactions it represents the local interaction distance or distance within which electrostatic 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 6 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 43 energy al cutoff distance Figure 2 Graph showing an electrostatic potential with and without the application of the shifting function z direct at 5 every step q 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 DPMTA 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 swit
145. 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 71 8 User Defined Forces There are several ways to apply external forces to simulations with NAMD These are described below 8 1 Constant Forces NAMD provides the ability to apply constant forces to some atoms There are two 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 mol A The occupancy O serves as
146. ion 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 70 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 without causing the pairlist to be
147. ion The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeY should have only small integer factors 2 3 and 5 46 e PMEGridSizeZ lt number of grid points in z dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeZ should have only small integer factors 2 3 and 5 e 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 e 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 e FFTWUseWisdom lt Use FFTW 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 sam
148. irst 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 second 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 Def
149. is at Urbana Champaign has created its molecular dynamics software NAMD developed by the Theoretical Biophysics Group TBG at Illinois 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 available from the NAMD 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 Registration Individuals may register in their own name or with their institutional or corporate affiliations Registration information must include 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
150. is 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 param value as well as param value This is supported but only before the first run command For an easy life use param value 17 2 2 3 Required NAMD configuration parameters The following parameters are required for every NAMD simulation e numsteps page 57 e coordinates page 20 e structure page 20 e parameters page 20 e exclude page 45 e outputname page 21 e one of the following three temperature page 58 velocities page 20 binvelocities page 21 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 18 3 Input and Output Files NAMD was developed to be compatible with existing molecular dynamics packages especially the packages X PLOR 9 and CHARMM 8 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
151. is not declared specifically then the pdb file specified by coordinates is utilized for this information fepCol tiCol lt Column in the fepFile tiFile 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 fepOutFreq tidutFreq lt Frequency of free energy output in time steps gt Acceptable Values positive integer Default Value 5 Description Every fepOutFreq tiOutFreq number of MD steps the output file fepOutFile tiOutFile is updated by dumping energies that are used for ensemble aver aging This variable could be set to 1 to include all the configurations for ensemble averaging Yet it is recommended to update fep0utFile ti0utFile energies at longer intervals to avoid large files containing highly correlated data unless a post treatment e g Bennett s acceptance ratio BAR 3 or simple overlap sampling SOS 32 is to be performed fepOutFile ti0utFile lt Alchemical free energy output filename gt Acceptable Values filename Default Value outfilename Description An output file named fepOutFile containing the FEP energies or tiOutFile containin
152. 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 Registration will be administered by the NAMD development team 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 Biophysics Group TBG 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 restricted 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
153. is rotated around its center of mass to optimally reproduce the coordinates given by refPositions or refPositionsFile This is done before recentering the group if centerReference is also defined The algorithm used is the same employed in the orientation colvar component 15 Forces applied to this group from within the colvar module are rotated back to the reference frame of the simulation prior being communicated to the MD integrator Note care must be taken when a torque is applied on the group which could bring the simulation out of control to avoid such problems disableForces could be used for this group refPositions lt atom group Reference positions for the group A gt Acceptable Values space separated list of x y z triplets Description If either centerReference or rotateReference is on these coordinates are used to determine the center of mass translation and the optimal rotation between them and the current coordinates of the group In the latter case the list must be of the same length as this atom group refPositionsFile lt atom group Reference positions for the group gt Acceptable Values UNIX filename Description If either centerReference or rotateReference is on the coordinates from this file are used to determine the center of mass s translation and the optimal rotation between them and the current coordinates of the group This file can either contain as 104 many atoms as the group in which c
154. ject 1 class gridpositions counts xn yn zn origin xorg yorg zorg delta xidel yldel zidel delta x2del y2del z2del delta x3del y3del z3del object 2 class gridconnections counts xn yn zn object 3 class array type double rank O items xn yn zn data follows f1 f2 f3 f4 f5 f6 Each axis of the grid may be specified as continuous or not If the grid is not continuous in a particular axis the potential grid is padded with three border slices 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 axis atoms outside the grid are affected by a potential that is interpolated from the grid and its corresponding periodic image along that axis 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 73 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 numerically approximating the gradient of the potential using 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 gri
155. keH 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 49 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 3 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 Specifies 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 expone
156. keyword value e Tcl commands and syntax are not allowed e for keywords with a boolean value in addition to the values yes on true and no off false the keyword without any value evaluates as on Options like global0ption define general features of the colvars module and are described in the following The options for the colvar blocks are documented in 9 2 and those for the colvar biases blocks biastype1 biastype2 in 9 3 91 collective variables config file globalOption value colvar 1 name ist colvar needed to identify the variable flags to define the behavior of 1st colvar colvarOptioni valuel colvarOption2 value2 all the following terms are summed together to provide the value of ist colvar componenttypel configuration for the 1st colvar component componentOption value componentLongOption componenttype2 colvar name 2nd colvar biastypel name mybias1 colvars ist colvar 2nd colvar biastype2 Figure 7 A typical colvars configuration file e colvarsTrajFrequency lt global Colvar value trajectory frequency gt Acceptable Values positive integer Default Value 1 Description The values of each colvar and any additional quantities which have been set to be reported are written at this frequency to the file lt outputName gt colvars traj If the value is 0 the trajectory file is not written For optimization the output is buffered as is
157. l 83 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 phix 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 aid3 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 84 8 10 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 whethe
158. l 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 the 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 61 6 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 9 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 coeff
159. l 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 User feedback If you have problems installing or running NAMD after reading this document please send a complete description of the problem by email to namd ks uiuc edu If you discover and fix a problem not described in this manual we would appreciate if you would tell us about this as well so we can alert other users and incorporate the fix into the public distribution We are interested in making NAMD more useful to the molecular modeling community Your suggestions are welcome at namd ks uiuc edu We also appreciate hearing about how you are using NAMD in your work 1 3 Acknowledgments This work is supported by grants from the National Science Foundation BIR 9318159 and the National Institute of Health PHS 5 P41 RR05969 04 13 The authors would particularly lik
160. lation 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 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 e 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 e 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 e BerendsenPressureRelaxationTime lt relaxation time fs gt Acceptable Values positive decimal Description Specifies relaxation time for Berendsen s method If the instantaneous pres sure did no
161. le 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 warning 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 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 g
162. le and langevinCol can optionally be set to control the behavior of this feature e langevinTemp lt temperature for Langevin calculations K gt Acceptable Values 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 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 langevinCo
163. lue cutoff molly lt use mollified impulse method MOLLY gt Acceptable Values on or off Default Value off Description This method eliminates the components of the long range electrostatic forces which contribute to resonance along bonds to hydrogen atoms allowing a fullElect Frequency 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 mollyTolerance lt allowable error for MOLLY gt Acceptable Values positive decimal Default Value 0 00001 Description Convergence criterion for MOLLY algorithm mollyIterations lt maximum MOLLY iterations gt Acceptable Values positive integer Default Value 100 Description Maximum number of iterations for MOLLY algorithm 60 6 4 Temperature Control and Equilibration 6 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 9 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 langevinFi
164. lues positive decimal Default Value 1 0 Description Defines the force constant for the extendedLagrangian mode The physical unit is the same as lowerWallConstant 95 e fictitiousMass lt colvar Fictitious mass of the colvar amu gt Acceptable Values positive decimal Default Value 1 0 Description Sets the fictitious inertial mass of this colvar 9 2 1 Collective variable components Each colvar has one or more components each of them defined by a functional form the atom positions from which it is calculated and any additional parameters of the functional form This section lists the types of components and their parameters Each component makes use of one or more atom groups whose syntax of definition is by their name followed by a definition block e g myatoms the options in the definition block are described in 9 2 3 Component distance distance between two groups The distance block defines a distance component between two atom groups group1 and group2 e groupl lt distance First group of atoms gt Acceptable Values Block group1 Description First group of atoms e group2 lt distance Second group of atoms gt Acceptable Values Block group2 Description Second group of atoms e oneSiteSystemForce lt distance Measure system force on group 1 only gt Acceptable Values boolean Default Value no Description If this is set to yes the system force is measured along a ve
165. mass drift 6 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 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 abov
166. 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 4 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
167. mine 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 68 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 the cutoff so that pairs are allowed
168. n 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 pressure 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 s
169. n 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 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 followin
170. n this file Non targeted atoms are ignored e TMDFirstStep lt first TMD timestep gt Acceptable Values Positive integer Default Value 0 Description e 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 78 e TMDInitialRMSD lt target RMSD at first TMD step gt Acceptable Values Non negative value in 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 e 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 towards 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 8 7 Steered Molecular Dynamics SMD The SMD feature is independent from th
171. nate 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 5 33 aimed at a gradual scaling of the short range nonbonded interactions of incoming atoms with their environment as shown in Equation 28 What 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 Rmin 2 3 V io A ij ij ij e ec n 28 NB rij LJEij 0 1 wa gt 6 1 5 ic It is also worth noting that the free energy calculation does not alter intermolecular bonded potentials e g
172. nd colvar component on the same atoms The options recognized within the alpha block are e residueRange lt alpha Potential a helical residues gt 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 be defined The colvar module looks for the atoms within these residues named CA N and O and raises an error if any of those atoms is not found e psfSegID lt alpha PSF segment identifier gt Acceptable Values string max 4 characters Description This option sets the PSF segment identifier for the residues specified in residueRange This option need not be provided when non PSF topologies are used by NAMD e hBondCoeff lt alpha Coefficient for the hydrogen bond term gt Acceptable Values positive between 0 and 1 Default Value 0 5 Description This number specifies the contribution to the total value from the hydrogen bond terms 0 will disable the hydrogen bond terms 1 will disable the angle terms e angleRef lt alpha Reference Ca Ca Ca angle gt Acceptable Values positive decimal Default Value 88 Description This option sets the reference angle used in the score function 18 101 e angleTol lt alpha Tolerance in the Ca Ca Ca angle gt Acceptable Values positive decimal Default Value 15 Description This option sets the angle tolerance use
173. ng parameter 24 output Value parameter 95 output Velocity parameter 95 pairInteraction parameter 132 pairInteractionCol parameter 132 pairInteractionFile parameter 132 pairInteractionGroup1 parameter 132 pairInteractionGroup2 parameter 132 pairInteractionSelf parameter 132 pairlistdist parameter 69 pairlistGrow parameter 71 pairlistMinProcs parameter 70 pairlistShrink parameter 71 pairlistsPerCycle parameter 70 pairlistTrigger parameter 71 parameters parameter 20 paraTypeCharmm parameter 20 paraTypeXplor parameter 20 parmfile parameter 24 patch psfgen command 37 pdb psfgen command 36 pdbalias atom psfgen command 39 pdbalias residue psfgen command 35 PME parameter 46 PMEGridSizeX parameter 46 PMEGridSizeY parameter 46 PMEGridSizeZ parameter 47 PMEGridSpacing parameter 46 PMElInterpOrder parameter 46 PMEProcessors parameter 47 PMETolerance parameter 46 PRESSAVG 23 pressureProfile parameter 133 pressureProfileAtomTypes parameter 134 pressureProfileAtomTypesCol parameter 135 pressureProfileAtomTypesFile parameter 135 pressureProfileEwald parameter 134 pressureProfileEwaldX parameter 134 pressureProfileEwald Y parameter 134 pressureProfileEwaldZ parameter 134 pressureProfileFreq parameter 134 pressureProfileSlabs parameter 133 print command 16 psfcontext create psfgen command 38 psfcontext delete psfgen command 38 psfcontext eval psfgen command 38 psfcontext psfgen command 38 ps
174. 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 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 gradient 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 ze
175. nsformation methods in NAMD e lambda tilambda 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 lambda2 Not applicable 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 sampling in the next window The free energy difference between lambda2 and lambda is calculated Through simulations at progressive values of lambda and lambda2 the total free energy difference may be determined e fepEquilSteps tiEquilSteps 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 fepEquilSteps tiEquilSteps 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 fepFile tiFile lt pdb file with perturbation flags gt Acceptable Values filename Default Value coordinates Description pdb file to be used for indicating the status of all atoms pertaining to the 120 system with respect to the alchemical transformation If this parameter
176. nt 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 atom should not be constrained Otherwise the value specified is used as the force constant for that atom s restraining potential 50 e constraintScaling lt scaling factor for harmonic constraint energy function gt Acceptable Values positive Default Value 1 0 Description The
177. ny set of colvars using different sampling methods currently implemented are the Adaptive Biasing Force ABF method see 9 3 1 metadynamics see 9 3 2 and Steered Molecular Dynamics SMD see 9 3 3 any number of harmonic restraints can also be applied to the colvars see 9 3 3 e calculate statistical properties of an individual collective variable along a simulated trajectory such as its running average standard deviation or the time auto correlation function ACF of its value its velocity or its total force see 9 2 4 e perform multidimensional correlation analysis by calculating frequency histograms of any subset of colvars 9 1 General parameters and input output files The structure of a typical collective variables calculation is depicted in Figure 6 Each colvar is a combination of one or more components see 9 2 which are functions of several atomic coordinates Multiple biasing or analysis methods can be applied to the same colvars But care should be taken that certain methods such as free energy reconstruction do not function properly if other biases are adding forces to their colvars The features described in this section were contributed by Giacomo Fiorin and J r me H nin Center for Molec ular Modeling University of Pennsylvania Philadelphia PA USA 89 biases colvars components distance d atoms 1 2 3 5 C 1 0 p 1 colvar d d d i 113 harm
178. o 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 10 133 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 Ewald 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 pre
179. of samples in a bin prior to application of the ABF gt Acceptable Values positive integer 109 Default Value 200 Description To avoid nonequilibrium effects in the dynamics of the system due to large fluctuations of the force exerted along the reaction coordinate it is recommended to apply the biasing force only after a reasonable estimate of the latter has been obtained e hideJacobian lt ABF Remove geometric entropy term from calculated free energy gradi ent gt 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 re sults 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 remov ing 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 ABF Frequency in timesteps at which ABF data files are refreshed gt Acceptable Values positive integer Default Value Colvar module restart frequency Description The files containing the free energy gradient estimate and the sampling histogram and the PMF if
180. of the free energy along a reaction coordinate in cartesian coordinates J Chem Phys 112 7283 7292 2000 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 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 H Grubmiiller Predicting slow structural transitions in macromolecular systems Conforma tional flooding Phys Rev E 52 3 2893 2906 Sep 1995 J H nin and C Chipot Overcoming free energy barriers using unconstrained molecular dynamics simulations J Chem Phys 121 2904 2914 2004 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 G Hummer and I Kevrekidis Coarse molecular dynamics of a peptide fragment Free energy kinetics and long time dynamics computations Journal of Chemical Physics 118 23 10762 10773 JUN 15 2003 W Humphrey and A Dalke VMD user guide Version 0 94 Beckman Institute Technical Report TB 94 07 University of Illinois 1994 M lannuzzi A Laio and M Parrinello Effi
181. 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 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 to store coordinate or velocity data being input or output from 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 3 1 2 X PLOR format PSF files NAMD uses the same protein structure files that X PLOR does At this time the easiest way to generate these files is using X PLOR or CHARMM although it is possible to build them by hand CHARMM can generate an X PLOR format PSF file with the command write psf card xplor 3 13 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 CHARM
182. oms 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 integer Default Value 2 Descript
183. on fepout Output file containing the free energy fepOutFreq E Frequency at which fepOutFreq is updated fepEquilSteps 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 OX while LambdaO lt 1 0 4 lambda Lambda0 set Lambda0 expr LambdaO dLambda TCL script to increment A 1 set lambda value 2 increment A lambda2 Lambda0 3 set lambda2 value il 10000 4 run 10 000 MD steps 123 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 30 will be computed over 5 000 MD steps Alternatively A states may be declared explicitly avoiding the use of TCL scripting lambda 0 0 1 set lambda value lambda2 0 1 2 set lambda2 value run 10000 3 run 10 000 MD steps This option is generally preferred to set up windows of diminishing widths as A 0 or 1 a way to circumvent end point singularities caused by appearing atoms that may clash with their surroundings The following second input is proposed for the measuring via TI the free energy of a particle insertion thermInt On Enable thermodynamic integration tiFile ion alch pdb PDB file with perturbation flags tiCol B Perturbation flags in Beta column tidutfile ion ti out tidutFreq 5 tiEquilSteps 5000 tiVdWShiftCoeff 1
184. on 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 Constant pressure molecular dynamics simulation The Langevin piston method J Chem Phys 103 11 1995 The equations of motion are r p m er p F ep gp R V 3Ve e 3V W P Po gee Re W W 3NT kT 2mgkT h T oscillationperiod lt R gt 2WgekT h A a N V l 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 target pressure bar gt
185. onic restraint distance d Yo 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 Example of a collective variables colvar configuration The colvar d is defined as the difference between two distances each calculated between the centers of mass of two atom groups The second colvar c holds the coordination number i e the number of contacts within a radius of 6 A between two groups The third colvar alpha measures the degree of a helicity of the protein segment between residues 1 and 10 A moving harmonic restraint is applied to the colvars d and c each rescaled by means of width parameters wg and we the centers of the restraint dg and co evolve with the simulation time t The histogram of alpha and c is also recorded on the fly 9 1 1 NAMD parameters To enable a colvar calculation the NAMD configuration file must set two parameters three when restarting a previous run e colvars lt Enable the collective variables module gt Acceptable Values boolean Default Value off Description If this flag is on the collective variables module within NAMD is executed at each time step the module requires a separate configuration file to be provided with
186. 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 A 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 A 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 pairlistdist parameter is also used to deter
187. ons as detailed in Section 6 3 4 DPMTA is no longer included in released binaries e FMALevels lt number of levels to use in multipole expansion gt Acceptable Values positive integer Default Value 5 Description Number of levels to use for the multipole expansion This parameter is only used if FMA is set to on A value of 4 should be sufficient for systems with less than 10 000 atoms A value of 5 or greater should be used for larger systems e FMAMp lt number of multipole terms to use for FMA gt Acceptable Values positive integer Default Value 8 Description Number of terms to use in the multipole expansion This parameter is only used if FMA is set to on If the FMAFFT is set to on then this value must be a multiple of 4 The default value of 8 should be suitable for most applications 48 e FMAFFT lt use DPMTA FFT enhancement gt Acceptable Values on or off Default Value on Description Specifies whether or not the DPMTA code should use the FFT enhancement feature This parameter is only used if FMA is set to on If FMAFFT is set to on the value of FMAMp must be set to a multiple of 4 This feature offers substantial benefits only for values of FMAMp of 8 or greater This feature will substantially increase the amount of memory used by DPMTA e FMAtheta lt DPMTA theta parameter radians gt Acceptable Values decimal Default Value 0 715 Description This parameter specifies the value of the theta parameter use
188. opology 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 8 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 Christophe 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 117 A al al Na NS e o Ce H KA E Figure 8 Dual topology description for an alchemical simulation Case example of the mutation of alanine into serine The lighter color denotes the non interacting alter
189. ordnun hBond alpha iv 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 by distanceZ In the general case the user should determine according to which type of calculation is being performed whether wrapA11 or wrapWater can be enabled e The colvars calculation is is not parallelized over the computational nodes Therefore the extra load on the first node where the colvars module is executed should be maintained lower than that of any other node In most cases this condition is very well satisfied but there may be some specific configurations for which such extra load may affect the parallel performance of NAMD As a general guideline an atom group should include for a large fraction of the whole system only when necessary 9 2 4 Statistical analysis of individual collective variables When the global keyword analysis is defined in the configuration file 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 colvar Calculate a time correlation function gt Acceptable Values boolean Default Value off Description Whether or not a time correlaction function should be calculated for this colvar e corrFuncWithColvar lt colvar Colvar name for
190. parameter 48 MAFFT parameter 49 MAFFTBlock parameter 49 MALevels parameter 48 MAMp parameter 48 MAtheta parameter 49 forceConstant parameter 115 FullDirect parameter 47 fullElectFrequency parameter 59 fullSamples parameter 109 F F F F F F GPRESSAVG 23 GPRESSURE 23 gridsUpdateFrequency parameter 113 grocoorfile parameter 27 gromacs parameter 26 grotopfile parameter 27 groupl parameter 96 group2 parameter 96 group2CenterOnly parameter 99 guesscoord psfgen command 39 hBondCoeff parameter 101 hBondCutoff parameter 102 hBondExpDenom parameter 102 hBondExpNumer parameter 102 hgroupCutoff A parameter 70 hideJacobian parameter 110 hillWeight parameter 113 hillWidth parameter 114 IMDfreq parameter 81 IMDignore parameter 81 IMDon parameter 80 IMDport parameter 80 IMDwait parameter 81 inputPrefix parameter 110 lambda tilambda parameter 120 lambda2 Not applicable parameter 120 langevin parameter 61 langevinCol parameter 61 langevinDamping parameter 61 langevinFile parameter 61 langevinHydrogen parameter 61 LangevinPiston parameter 66 LangevinPistonDecay parameter 66 LangevinPistonPeriod parameter 66 LangevinPistonTarget parameter 66 LangevinPistonTemp parameter 67 langevinTemp parameter 61 last psfgen command 36 les parameter 128 lesCol parameter 129 lesFactor parameter 128 lesFile parameter 129 lesReduceMass parameter 129 lesReduceTemp paramete
191. 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 64 6 5 1 Berendsen pressure bath coupling NAMD provides constant pressure simu
192. put 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 79 Parameters The following parameters describe the parameters for the SMD feature of NAMD e 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 e 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 structure or coordinate file since the atom number field in this PDB file will be ignored e SMDk lt force constant to use in SMD simulation gt Acceptable Values positive real D
193. r 128 limitdist parameter 45 longSplitting parameter 60 lowerBoundary parameter 94 lower WallConstant parameter 94 main parameter 96 margin parameter 70 margin violations 68 maximumMove parameter 57 measure command 17 mergeCrossterms parameter 23 meridforce parameter 74 meridforcecol parameter 74 meridforcecontl parameter 75 meridforcecont2 parameter 75 meridforcecont3 parameter 75 meridforcefile parameter 74 megridforceqcol parameter 74 meridforcescale parameter 74 meridforcevfile parameter 74 meridforcevoff parameter 75 meridforcevolts parameter 74 minBabyStep parameter 57 minimization parameter 57 minimize command 16 minLineGoal parameter 57 minTinyStep parameter 57 MISC energy 23 molly parameter 60 mollyIterations parameter 60 mollyTolerance parameter 60 movingConstraints parameter 76 movingConsVel parameter 76 MTSAlgorithm parameter 60 multipleReplicas parameter 114 154 multiply psfgen command 37 mutate psfgen command 37 name parameter 94 107 113 newHillFrequency parameter 113 nonbondedFreq parameter 59 nonbondedScaling parameter 45 numsteps parameter 57 oneSiteSystemForce parameter 96 98 OPLS 45 output command 16 outputAppliedForce parameter 95 outputEnergies parameter 23 outputFreq parameter 110 116 outputMomenta parameter 23 outputname parameter 21 outputPairlists parameter 71 outputPressure parameter 23 outputSystemForce parameter 95 outputTimi
194. r add it to your login or batch script You must be able to connect 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 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 directo
195. r 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 tclBC 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 tc1BC 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 me
196. rameters such as colvars a histogram block may define the following parameter e outputFreg lt histogram Frequency in timesteps at which the histogram file is refreshed gt Acceptable Values positive integer Default Value Colvar module restart frequency Description The file containing histogram data is written on disk at the given time interval Like the ABF bias the histogram feature uses parameters from collective variables to define its grid The grid ranges from lowerBoundary to upperBoundary and the bin width is set by the width parameter 116 10 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 thermodynamic integration TI 10 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 13 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
197. ration file and set 1 4scaling to the inverse value of SCEE as would be used in AMBER 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 switching 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 amp cntrl 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 Resta
198. rator exponent gt Acceptable Values positive even integer Default Value 6 Description This number defines the n exponent for the switching function e expDenom lt coordnum Denominator exponent gt Acceptable Values positive even integer Default Value 12 Description This number defines the m exponent for the switching function e cutoff3 lt coordnum Reference distance vector A gt Acceptable Values x y z triplet of positive decimals Default 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 98 e group2CenterOnly lt coordnum Use only group2 s center of mass gt Acceptable Values boolean Default Value off Description If this option is on only contacts between the 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 This component returns a dimensionless number which ranges from approximately 0 all inter atomic distances much larger than the cutoff to Ngroup1 Ngroup2 all distances within the cutoff or Negroupi if group2CenterOnly is used As a recommendation at least one group1 and group2 should be of limited size unless group2CenterOnly is used because the size of the loop over all pairs grows with the product of the sizes of group1 and group2 Component hBond hydrogen bond between t
199. rdinates to be assigned Context After structure has been generated coordpdb lt file name gt segid 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 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 guesses 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 39 e writepdb lt file name gt Purpose Writes PDB file containing coordinates Atoms order is identical to PSF file generated by writepsf unless structure has been changed The O field is set to 1 for atoms with known coordinates O 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 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
200. rds e forceConstant lt harmonic Harmonic force constant kcal mol gt Acceptable Values positive decimal Default Value 1 0 Description This defines the constant for the harmonic potential In order to cope with multidimensional restraints it is scaled by the square of the specific width for each colvar involved For instance a force constant of 10 kcal mol acting on a dihedral colvar with a width of 2 degrees will amount effectively to 2 5 kcal molxdegree e centers lt harmonic Harmonic restraints centers gt Acceptable Values space separated list of colvar values Description The centers of the restraint are entered here and must be of the same number of the requested colvars Each value is in the format of 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 qi q2 q3 quadruplet if it return a rotational quaternion If a colvar has periodicities or symmetries its closest image to the restraint center is assumed when calculating the harmonic potential e targets lt harmonic Harmonic restraints centers gt Acceptable Values space separated list of colvar values Description When defined the current centers will be moved towards these values in targetsNumSteps steps by a linear interpolation The intermediate values will be evolved by taking into account periodicities or symmetries the closest image of the target is assumed
201. re that data is read properly e readBegin lt global analysis mode Only read frames from this step gt Acceptable Values positive integer Default Value 0 Description If readTrajectory is defined only lines starting from this step number are actually loaded by the colvars e readEnd lt global analysis mode Only read frames up to this step gt Acceptable Values positive integer Default Value 0 Description If readTrajectory is defined and this number is larger than readBegin only lines up to and including this step number are actually loaded in the colvars 9 2 Declaring and using collective variables Each collective variable is defined as a combination of individual quantities called components see Figure 6 To obtain a colvar r its components q r are summed according to le gt cilas e 12 1 where each component appears with a unique coefficient c and positive integer exponent ni Note in most applications only one component per colvar needs to be defined accordingly c and ni are equal to 1 by default In the configuration file a collective variable is initiated by the keyword colvar followed by its configuration options usually between curly braces colvar Each variable must have one or more components defined by blocks specifying a functional form atoms whose coordinates are used to evaluate this functional form and optional parameters as needed Each component block is initia
202. 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 multiply lt factor gt lt segid resid atomname 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 tools Arguments lt factor gt lt segid resid atomname gt segment residue or atom to be multiplied If resid is omitted the 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
203. rk is that the moving reference position is calculated ev ery integration time step using Eq 8 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 xo and the force with F dk x xo where d is the exponent consexp The result is that if one specifies some 75 22 20 4 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 points 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 value for the force constant k in the PDB file ef
204. ro 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 111 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 9 3 2 Metadynamics calculations Many methods have been introduced in the past that make use of an artificial energy term that changes and adapts over time to reconstruct a potential of mean force from a conventional molec ular dynamics simulation 24 22 45 16 31 25 One of the most recent metad
205. rom 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 resname gt Residue type name from topology file lt chain gt Single character chain identi fier Context Anywhere within segment 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
206. rosses 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 to the origin providing hexagonal or other cell shapes 6 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 sphericalBCr1 lt radius for first boundary condition A gt Acceptable Values positive decimal Description Distance at whi
207. roviding an estimate of the free energy gradient according to equation 20 The biasing force applied along the colective variables to overcome free energy barriers is calculated as 108 FABF e A E 24 where V A denotes the current estimate of the free energy gradient at the current point in the collective variable subspace 7 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 dihedral gyration and rmsd 3 Mutual orthogonality of colvars In a multidimensional ABF calculation equation 21 must be satisfied for any two colvars and Various cases fulfill this ortho
208. rt 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 exclude 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 25 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 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
209. rts a maximum of 15 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 correctly 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 0 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 11 1 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 o
210. ry Some automounters use a temporary mount directory which 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 145 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 15 3 Windows Workstation Networks These are no longer supported but NAMD has been reported to compile on Windows HPC Server
211. s F 2kK R X 1 keal mol A 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 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 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 e 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 e rotConsVel lt Angular velocity of rotation gt Acceptable Values rate in degrees per timestep TT Description Angular velocity of rotation degrees timestep 8 6 Targeted Molecular Dynamics TMD In TMD subset of atoms in the simulation is guided towards 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 c
212. s RMS of roughly 100 63 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 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 non printed intermediate steps If you
213. s 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 for excluded and 0 for not exclu
214. sary 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 system see Figure 11 126 10 12 log dE dl 0 0 NS S SS S SS S S a 0 4 0 lambda Figure 11 Sample TI data log ov against A The blue shaded area shows the integral with fine sampling close to the end point The red area shows the difference when values are more sparse In this example insufficient sampling before A 0 1 can result in a large overestimation of the integral Beyond 0 2 sparser sampling is justified as dE dA is not changing quickly 127 11 Accelerated Sampling Methods 11 1 Locally enhanced sampling Locally enhanced sampling LES 38 40 41 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 11 1 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 suppo
215. set set set set set set set set set set set set num_replicas 8 min_temp 300 max_temp 600 steps_per_run 1000 num_runs 10000 runs_per_frame 10 frames_per_restart 10 namd_config_ file alanin_base namd output_root output fold_alanin directory must exist psf_file alanin psf initial_pdb_file unfolded pdb fit_pdb_file alanin pdb namd_bin_dir Projects namd2 bin current Linux64 server_port 3177 spawn_namd_command list spawn_namd_ssh cd pwd file join namd_bin_dir namd2 netpoll A list beirut belfast 131 12 Runtime Analysis 12 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 The 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
216. single machine like a multicore build or across a network 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 namd2 local p lt procs gt lt configfile gt You may need to specify the full path to the namd2 binary 144 15 2 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 o
217. ssages 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 cell0rigin e nearest the equivalent position nearest to the cell0rigin The following commands are available from within the calcforces procedure 85 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 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
218. ssureProfileEwaldX 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 profile 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 134 e pressureProfileAtomTypesFile lt Atom type partition assignments gt
219. 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 Tcl too e the print command to display messages puts is broken sorry e environment variables through the env array Senv USER and e user defined variables set base sim23 dedfile 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 e The minimize command is similar to run and performs minimization for the specified number of force evaluations e The output command takes an output file basename and causes coor vel and xsc files to be written with that name S e 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 us
220. t 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 by 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 20 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 nam
221. t metadynamics Multiple replicas database file gt Acceptable Values UNIX filename Default Value lt name gt replica_files txt Description If multipleReplicas is on this option sets the path to a replica index file The names of new hill files containing other replica s new hills are appended to the contents 114 of this file Every replicaUpdateFrequency steps during a simulation each replica reads the hills stored in each of the files listed here except those saved by the replica itself e replicaUpdateFrequency lt metadynamics Multiple replicas update frequency gt Acceptable Values positive integer Default Value newHillFrequency Description If multipleReplicas is on this option sets the number of steps between updates of the list of hills created by other replicas e writeHillsTrajectory lt metadynamics Write a log of new hills gt Acceptable Values boolean Default Value on Description If this option is on a logfile is written by the metadynamics bias with the name lt outputName gt colvars lt name gt hills traj which can be useful to follow the time series of the hills When multipleReplicas is on its name changes to lt outputName gt colvars lt name gt lt replicaID gt hills traj 9 3 3 Harmonic restraints and Steered Molecular Dynamics The harmonic restraint is allocated by a harmonic block which may contain in addition to the standard option colvars the following keywo
222. t available making the colvar unsuitable for ABF calculations e componentCoeff lt any component Coefficient of this component in the colvar gt 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 9 2 3 Defining atom groups Each component depends on one or more atom groups which can be defined by different methods in the configuration file Each atom group block is initiated by the name of the group itself within the component block followed by the instructions to the colvar module on how to select the atoms involved Here is an example configuration for an atom group called myatoms which makes use of the most common keywords 102 atom group definition myatoms add atoms 1 2 and 3 to this group note numbers start from 1 atomNumbers 123 add all the C alphas within residues 11 to 20 of segment PROT atomNameResidueRange CA 11 20 psfSegID PROT add all the atoms with occupancy 2 in the file atoms_occ1 pdb atomsFile atoms_occl1 pdb atomsCol 0 atomsColValue 2 0 For any atom group the available options are atomNumbers lt atom group List of atom numbers gt Acceptable Values space separated list of positive integers Description This option adds to the group all the atoms whose numbers are in the list Atom numbering starts from 1 atomNumbersRange lt
223. t 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 e 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 6 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 65 with a method of temperature control such as Langevin dynamics in order to simulate the NPT ensemble The Langevin pist
224. t 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 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 1802 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 through Dr Gila Budescu at the addresses listed below in Contact Information 7 Should Licensee wish to make commerci
225. t the variable to which this bias is applied the block accepts the following options e name lt metadynamics Name of this metadynamics instance gt Acceptable Values string Default Value meta rank number Description This option sets the name for this metadynamics instance While in general it is not advisable to use more than one metadynamics bias this allows to distinguish each bias from the others in the output e hillWeight lt metadynamics Height of each hill kcal mol gt Acceptable Values positive decimal Default Value 0 01 Description This option sets the height W of the hills that are added during this run e newHillFrequency lt metadynamics Frequency of hill creation gt Acceptable Values positive integer Default Value 100 Description This option sets the number of steps after which a new hill is added to the history dependent potential It acts on the colvars immediately after it has been added e useGrids lt metadynamics Optimize the hills calculation gt Acceptable Values boolean Default Value on Description This option discretizes all hills on two grids storing their total energy and gradients respectively The grids are defined by lowerBoundary upperBoundary and width for each colvar and are saved to the state file Currently this is implemented for non scalar variables only In this case writeHillsTrajectory may be useful to keep track of the history e gridsUpdateFrequency
226. ted within the colvar block by the keyword corresponding to a given functional form For 93 instance the block distance adds a component whose value is the distance between to atom groups The types of components used determine the properties of a colvar and which biases or analysis methods can be applied to it For instance the colvar returns a scalar value if it includes components of one or more of the following types distance distanceZ distanceXY angle dihedral coordnum hBond rmsd orientationAngle gyration and alphaHelix The colvar returns instead a three dimensional vector d if distanceVec is used a three dimensional vector with a d 1 constraint if distanceDir is used and a unitary quaternion used to parameterize a rotation if orientation is are used Currently binning of colvar values on a grid can only be performed for scalar components In addition some properties like the system force can be calculated only for some of these components The detail documentation all component types is provided in 9 2 1 Note restrictions only apply to the type of an individual colvar In fact all of the implemented methods can be applied to any number of collective variables Irrespective of which components it is built of each colvar can be provided the following parameters e name lt colvar Name of this colvar gt Acceptable Values string Default Value colvar numeric id Description The name is an uniqu
227. ter 22 DCDfreq parameter 22 DCDUnitCell parameter 22 decouple decouple parameter 123 delatom psfgen command 37 dielectric parameter 45 disableForces parameter 105 dummyAtom parameter 104 dumpFreeEnergyFile parameter 113 eField parameter 72 eFieldOn parameter 72 error message Atoms moving too fast 69 Bad global exclusion count 69 exclude parameter 45 ExcludeFromPressure parameter 67 ExcludeFromPressureCol parameter 67 ExcludeFromPressureFile parameter 67 expandGrids parameter 114 expDenom parameter 98 expNumer parameter 98 extCoordFilename parameter 88 extendedForceConstant parameter 95 extendedLagrangian parameter 95 extendedSystem parameter 53 extForceFilename parameter 88 extForces parameter 88 extForcesCommand parameter 88 fep thermInt parameter 120 fepCol tiCol parameter 121 fepElecLambdaStart tiElecLambdaStart pa rameter 121 fepEquilSteps tiEquilSteps parameter 120 fepFile tiFile parameter 120 fepOutFile tiOutFile parameter 121 fepOutFreq tiOutFreq parameter 121 fepVdwLambdaEnd tiVdwLambdaEnd pa rameter 122 fepVdwShiftCoeff tiVdwShiftCoeff parame ter 121 FFTWEstimate parameter 47 FFTWUseWisdom parameter 47 FFTWWisdomFile parameter 47 fictitiousMass parameter 96 first psfgen command 36 firsttimestep parameter 58 fixedAtoms parameter 51 fixedAtomsCol parameter 52 153 fixedAtomsFile parameter 52 fixedAtomsForces parameter 51 MA
228. 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 TBG 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 OF ANY KIND EITHER EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO WARRANTIES OR MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY PATENT TRADE MARK OR OTHER RIGHTS LICENSEE ASSUMES THE ENTIRE RISK AS TO THE RE SULTS AND PERFORMANC
229. the same format binary DCD as X PLOR If velDCDfile is defined then velDCDfreq must also be defined 22 e 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 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 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
230. tion and Dynamics Parameters 6 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 8 10 6 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 cellBasisVector1 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions cellBasisVector2 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions cellBasisVector3 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions 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 extendedSystem lt XSC file to read cell parameters from gt Acceptable Values file name Description In addition to coor and vel output files NAMD gen
231. to it This is different from psfcontext 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 38 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 Us
232. tor 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 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 0 142 incr ts 1000 coorfile close 143 15 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 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 namd
233. tput a system force trajectory for this colvar gt Acceptable Values boolean Default Value off Description If colvarsTrajFrequency is defined and all components support its cal culation the total system force on this colvar i e the projection of all interatomic forces except constraint forces on this colvar see equation 23 in section 9 3 1 are written to the trajectory file under the label fs_ lt name gt The physical unit for this force is kcal mol divided by the colvar unit outputAppliedForce lt colvar Output an applied force trajectory for this colvar gt Acceptable Values boolean Default Value off Description If colvarsTrajFrequency is defined the total force applied on this colvar by biases within the colvar module are written to the trajectory under the label fa_ lt name gt The physical unit for this force is kcal mol divided by the colvar unit extendedLagrangian lt colvar Add an extra degree of freedom gt Acceptable Values boolean Default Value off Description Adds a fictitious particle with mass fictitiousMass coupled to the colvar by a harmonic potential with force constant extendedForceConstant Biasing forces on the colvar are applied to this extra particle rather than to the atoms directly This implements the extended Lagrangian formalism used in some metadynamics simulations 27 extendedForceConstant lt colvar Ext Lagrangian force constant kcal mol gt Acceptable Va
234. tput 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 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 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 t
235. ts than ASCII PDB files but the binary files are not guaranteed to be transportable between computer architectures The utility program flipbinpdb is provided with the Linux Intel version to reformat these files e restartname lt restart files gt Acceptable Values UNIX filename prefix Description The prefix to use for restart filenames NAMD produces PDB restart files 21 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 If restartfreq is defined then restartname must also be defined 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 Activates the use of binary restart files If this option is set to yes then the restart files will be written in binary rather than
236. tum conservation PME lt Use particle mesh Ewald for electrostatics gt Acceptable Values yes or no Default Value no Description Turns on particle mesh Ewald PMETolerance lt PME direct space tolerance gt Acceptable Values positive decimal Default Value 107 Description Affects the value of the Ewald coefficient and the overall accuracy of the results PMEInterpOrder lt PME interpolation order gt Acceptable Values positive integer 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 Descript
237. uld 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 147 16 NAMD Availability and Installation NAMD is distributed freely for non profit use NAMD 2 7b1 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 2 7b1 16 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 distributions are available 16 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 2 7b1 bin
238. urrent coordinates The force on each atom is given by the gradient of the potential Urmp RMS t RMS t 9 where RM S 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 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 9 A value of 200 seems to work well in many cases 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 where ts is the timestep targetRMS is the target RMSD at that timestep and currentRMS is the actual RMSD e TMDFile lt File for TMD information gt Acceptable Values Path to PDB file Description Target atoms are those whose occupancy O is nonzero in the TMD PDB file The file must contain the same number of atoms as the structure file The coordinates for the target structure are also taken from the targeted atoms i
239. using a positive value of 121 Decoupling Mutation elecLambdaStart 0 5 vdwLambdaEnd 1 0 elecLambdaStart 0 5 vdwLambdaEnd 0 7 ale o LEF o 2 2 Ss f S 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 10 Relationship of user defined A to coupling of electrostatic or vdW interactions to a simulation given specific values of elecLambdaStart or vdwLambdaEnd fepVdWShiftCoeff tiVdwShiftCoeff 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 In the current implementation the electrostatic interactions of an exnihilated or ap pearing particle are linearly coupled to the simulation over the A value range of fepElecLambdaStart tiElecLambdaStart 1 0 At A values less than or equal to the user defined value of fepElecLambdaStart tiElecLambdaStart electrostatic interactions of the exnihilated particle are fully decoupled from the simulation Coupling of electrostatic interac tions 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 lin early decoupled from the simulation over the A value range of 0 1 0 fepElecLambdaStart
240. ution to the long range electrostatic terms that require O N or O N log N computational cost depending on the method 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 42 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
241. value of the component is e r rm e axis lt distanceZ distanceXY Projection axis A gt 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 r The vector should be written as three components separated by commas and enclosed in parentheses e oneSiteSystemForce lt distanceZ distanceXY Measure system force on group main only gt Acceptable Values boolean Default Value no Description If this is set to yes the system force is measured along a vector field see equation 23 in section 9 3 1 that only involves atoms of main This option is only useful for ABF or custom biases that compute system forces See section 9 3 1 for details This component returns a number in A whose range is determined by the chosen boundary conditions if the z axis is used in PBC its value is limited between b 2 and b 2 where b is the box length in the z direction Component distanceXY projection of a distance on a plane The distanceXY block defines a distance projected on a plane and accepts the same options as 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 th
242. ve 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 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 81 print lt anything gt This command should be used instead of puts to display output For example print Hello World atomid lt segname gt lt resid gt lt atomname gt Determines atomid of an atom from its segment residue and name For example atomid br 2 N 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 NJ addgroup lt atomid list gt Request center of mass coordinates of this group for next force evaluation Returns a group ID whi
243. wo atoms The hBond block defines a hydrogen bond implemented as a coordination number eq 13 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 coordnun 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 Component rmsd root mean square displacement RMSD with respect to a reference structure The block rmsd defines the root mean square replacement RMSD of a group of atoms with respect to a reference structure For each set of coordinates x t xX2 t x t the colvar component rmsd calculates the optimal rotation U Ga 9 that best superimposes the coordinates x t onto a set of reference coordinates xD Both the current and the reference coordinates are centered on their centers of geometry Xcog t and ne The root mean square displacement is then defined as N RMSD xi t Ey 4 7 JU Gilt xeog t x0 xP 4 i 1 The optimal rotation U Ea O jg calculated within the formalism developed in reference 15 y ref A which guarantees a continuous dependence of UP u Vi kx with respect to x t The options for rmsd are e atoms lt rmsd Atom
244. y building NAMD against an SMP version of Charm such as net linux smp or net linux smp icc This will use a communication thread for each process to respond to network activity more rapidly For dual processor clusters we have found it that running two separate processes per node each with its own communication thread is faster than using the charmrun ppn option to run multiple worker threads However we have observed that when running on a single hyperthreaded processor i e a newer Pentium 4 there is an additional 15 boost from running standalone with two threads namd2 p2 beyond running two processors charmrun namd2 local p2 For a cluster of single processor hyperthreaded machines an SMP version should provide very good scaling running one process per node since the communication thread can run very efficiently on the second virtual processor We are unable to ship an SMP build for Linux due to portability problems with the Linux pthreads implementation needed by Charm Extremely short cycle lengths less than 10 steps will also limit parallel scaling since the atom migration at the end of each cycle sends many more messages than a normal force evaluation Increasing pairlistdist from e g cutoff 1 5 to cutoff 2 5 while also doubling stepspercycle from 10 to 20 may increase parallel scaling but it is important to measure When increasing stepspercycle also try increasing pairlistspercycle by the same proportion NAMD sho
245. yfile 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 pdb 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 29 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 badwat
246. ynamics was first designed as a step wise algorithm which may be roughly described as an adaptive umbrella sam pling 31 and was later transformed into a continuous one 27 The implementation described here provides the latter version only which is the most commonly used In metadynamics the external potential on the colvars 1 2 n is t lt t Ney E ANN Vineta amp y W exp 64 25 i 1 2 2 t 6t 26t g that is Vmeta is a history dependent potential which acts on the current values of the colvars and depends parametrically on the previous values of the colvars It is constructed as a sum of N y dimensional repulsive Gaussian hills with a height W their centers are located at the previously explored configurations dt 20t and they extend by approximately 20 in the direction of the i th colvar As the system evolves according to the underlying potential of mean force A incremented by the metadynamics potential Vineta new hills will tend to accumulate in the regions with a lower effective free energy A A Vneta That is the probability of having a given system configuration being explored and thus a hill being added there is proportional to exp Ate KBT which tends to a nearly flat histogram when the simulation is continued until the system has deposited hills across the whole free energy landscape In this situation

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