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1. 1 incr ts 500 firstTimestep ts run 0 coorfile close 6 13 Replica Exchange Simulations The lib 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 110 potenergy dat There is also a script to load the output into VMD and color each frame according to target temperature n example simulation folds a 66 atom model of a deca alanine helix in about 10ns This implementation is designed to be modified by the user to implement exchanges of pa rameters other than temperature or via other temperature exchange methods The scripts should provide a good starting point for any simulation method requiring a number of loosely interacting systems replica_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 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 scrip
2. Arguments Context At any time writepsf charmm x plor cmap nocmap lt file name gt Purpose Write out structure information as PSF file A simplified session log is listed in the REMARKS section of the PSF file Arguments charmm Use CHARMM format numbers for atom types x plor Use X PLOR format names for atom types the 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 co
3. 7 0 1 A velocity vector Y movingConsVel needs to be specified The way the moving constraints work is that the moving reference position is calculated ev ery integration time step using Eq 1 where Y 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 70 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 value for the force constant k in the PDB file effectively the force constant is 2k in calculations This caveat was removed in SMD feature The following parameters describe the parameters for the moving harmonic constraint feature of NAMD e movingConstraints lt Are moving constraints active gt Acceptable Values on or off Default Value off 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 dire
4. G 1 N1 40 0 30 0 dihei dihe A 1 01 A 1 CA A 1 02 G 1 N3 40 0 0 0 dihe2 f dihe A 1 CA A 1 02 G 1 N2 G 1 N3 40 0 0 0 The general syntax of an item of this list is name type atom1 atom2 atom3 atom4 k reference where name could be any word used to refer to the restraint in the NAMD output type is the type of restraint e a distance dist a valence angle angle or a dihedral angle dihe Definition of the successive atoms follows the syntax of NAMD conformation free energy calculations k is the force constant of the harmonic restraint the unit of which depends on type reference is the reference target value of the restrained coordinate Aside from dist angle and dihe which correspond to harmonic restraints linear ramps have been added for distances using the specific keyword distLin In this particular case generally useful in umbrella sampling free energy calculations the syntax is name distLin atoml atom2 F r1 r2 where F is the force in kcal mol A The restraint is applied over the interval between r1 and r2 The harm restraint applies onto one single atom a harmonic potential of the form V a y 2 1 1 1 5 kale ao 5 ly yo hala PE 2 This way atoms may be restrained to the vicinity of a plane an axis or a point depending on the number of nonzero force constants The syntax is name harm atom kx ky kz x0 yO z0 98 6 8 5 Important recommendations when running
5. NAMD User s Guide Version 2 6 M Bhandarkar R Brunner C Chipot A Dalke S Dixit P Grayson J Gullingsrud A Gursoy D Hardy J H nin W Humphrey D Hurwitz N Krawetz S Kumar M Nelson J Phillips A Shinozaki G Zheng F Zhu March 31 2008 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 6 Authors M Bhandarkar R Brunner C Chipot A Dalke S Dixit P Grayson J Gullingsrud A Gursoy D Hardy J H nin W Humphrey D Hurwitz N Krawetz S Kumar M Nelson J Phillips 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 Illinois 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 individual
6. e at both xiMin and xiMax to guarantee that sampling will be confined between these two values dSmooth lt Length over which force data is averaged when computing the ABF gt Acceptable Values positive decimal number in Default Value 0 0 Description To avoid abrupt variations in the average force and in the free energy fluctuations are smoothed out by means of a weighted running average over adjacent bins on each side of When the free energy derivative varies slowly smoothing can be performed across several contiguous bins Great attention should be paid however when the free energy varies sharply with fullSamples lt Number of samples in a bin prior to application of the ABF gt Acceptable Values positive integer 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 outFile lt Output file of an ABF calculation gt Acceptable Values Unix filename Default Value abf dat Description Output file containing for each value of the reaction coordinate the free energy A the average force F and the number of samples accrued in the bin historyFile lt History of the force data over time gt Acceptable Values Unix filename Default Value none Description
7. e g a solute 5 zCoord 1atom is similar to zCoord but using a single atom of interest abf1 list of indices of reference atoms abf2 index of an atom of interest 6 xyDistance is the distance between the centers of mass of two atom groups projected on the x y plane abf1 list of indices of atoms participating to the first center of mass abf2 list of indices of atoms participating to the second center of mass xiMin lt Lower bound of the reaction coordinate gt Acceptable Values decimal number in Description Lower limit of the reaction coordinate below which no sampling is per formed xiMax lt Upper bound of the reaction coordinate gt Acceptable Values decimal number in Description Upper limit of the reaction coordinate beyond which no sampling is performed dxi lt Width of the bins in which the forces are accumulated gt Acceptable Values decimal number in Description Width 6 of the bins in which the instantaneous components of the force Fe are collected The choice of this variable is dictated by the nature of the system and how rapidly the free energy changes as a function of forceConst lt Force constant applied at the borders of the reaction coordinate gt Acceptable Values positive decimal number in kcal mol A Default Value 10 0 Description If this force constant is nonzero a harmonic bias is enforced at the borders 95 of the reaction coordinate
8. e nonbondedFreq lt timesteps between nonbonded evaluation gt Acceptable Values positive integer factor of fullElectFrequency Default Value 1 Description This parameter specifies how often short range nonbonded interactions should be calculated Setting nonbondedFreq between 1 and fullElectFrequency allows triple timestepping where for example one could evaluate bonded forces every 1 fs short range nonbonded forces every 2 fs and long range electrostatics every 4 fs e MTSAlgorithm lt MTS algorithm to be used gt Acceptable Values impulse verletI or constant naive Default Value impulse Description Specifies the multiple timestep algorithm used to integrate the long and short range forces impulse verletl is the same as r RESPA constant naive is the stale force extrapolation method e longSplitting lt how should long and short range forces be split gt Acceptable Values 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 16 SW rij 0 if Fizl gt Roff SW rij 1 if ris lt Ron if Ross gt F 2 Ron where Ron is a constant defined using the configuration value switchdist Roy is specified using the configuration value cutoff 54 e molly lt use mollified impulse method MOLLY gt Acceptable Val
9. source lt path to gt lib abf abf tcl where lt path to gt lib abf abf tcl is the complete path to the main ABF file The other Tcl files of the ABF package must be located in the same directory A second option for loading the ABF module is to source the 1ib init tcl file distributed with NAMD and then use the Tcl package facility The file may be sourced in the config file source lt path to gt lib init tcl package require abf Or to make the config file portable the init file may be the first config file passed to NAMD namd2 lt path to gt lib init tcl myconfig namd and then the config file need only contain package require abf Note that the ABF code makes use of the TclForces and TclForcesScript commands As a result NAMD configuration files should not call the latter directly when running ABF 6 8 3 Parameters for ABF simulations The following parameters have been defined to control ABF calculations They may be set using the folowing syntax abf lt keyword gt lt value gt where lt value gt may be a number a word or a Tcl list Keywords are not case sensitive e coordinate lt Type of reaction coordinate used in the ABF simulation gt Acceptable Values distance distance com abscissa zCoord zCoord latom or xyDistance Description As a function of the system of interest a number of alternative reaction coordinates may be considered The ABF code is modular RC specific code for each RC is contained in a
10. 20 insulin 22 group ca insulin 30 to insulin 32 insulin 34 all insulin 35 barr 20 ref 90 Bound specifications 1 impose an upper bound if an atom s position strays too far from a reference position add an energy term if the atom is more than 10A from 2 0 2 0 2 0 2823 impose lower and upper bounds on the distance between the ca s of residues 5 and 15 if the separation is less than 5 0A or greater than 12 0A add an energy term 4 impose a lower bound on the angle between the centers of mass of residues 3 6 9 if the angle goes lower than 90 apply a restraining potential urestraint posi bound insulin 3 cb kf 20 hi 2 0 2 0 2 0 10 0 dist bound insulin 5 ca insulin 15 ca kf 20 low 5 0 dist bound insulin 5 ca insulin 15 ca kf 20 hi 12 0 angle bound insulin 3 insulin 6 insulin 9 kf 20 low 90 0 torsional bounds are defined as pairs this example specifies upper and lower bounds on the dihedral angle X separating the planes of the 1 2 3 residues and the 2 3 4 residues The energy is 0 for 90 jx 1202 The energy is 20 kcal mol for 130 x 260 Energy rises from 0 20 kcal mol as x increases from 120 130 and decreases from 90 100 88 urestraint dihe bound insulin 1 insulin 2 insulin 3 insulin 4 gap 20 low 90 hi 120 delta 10 Forcing restraints a forcing restraint will
11. Ky 2 Tref T JR yi a Yref F 2 Zref E Gradient for stretch restraint E Ky 2 di dyef o di z2 21 9 91 22 21 V E K di dref V di for atom 2 moving and atom 1 fixed 1 2 V di 1 2 2 a1 yo y1 2 2 lam 2 yo y1 2 22 21 V di 22 21 T y2 y1 F 2 2 F d V E Ky di dres di 22 21 T 2 11 F 22 21 K Gradient for bend restraint E Ky 2 0 es Atoms at positions A B C distances A to B c A to C b B to C a 6 cos u cos a c b 2ac V E Ky 0 Ores V 05 V 0 Fam V for atom A moving atoms B amp C fixed distances b and c change V u b ac V b a 2c 1 2a b 2a V c V b z4 zc T va yc F 24 zc E b V c z4 zB T ya yB Y z4 zB E c for atom B moving atoms A amp C fized distances a and c change V u 1 2c c 2a b 2a c V a a 22 1 2a b 2ac V c V a zp zo yB vc zB zc k a V c zB za uB ya T zB 2a F c for atom C moving atoms A amp B fized distances a and b change V u b ac V b c 2a 1 2c b 2a V a V b zo za yc ya F 20 24 k b V a zc zB yc ya F zc zn F a Gradient for
12. N AAq 5 Y In exp 8 H x Pa Mi 1 H X Pa Xi 9 i 1 Here N stands for the number of intermediate stages or windows between the initial and the final states see Figure 5 100 Co D E D X a X b X c Py Figure 5 Convergence of an FEP calculation If the ensembles representative of states a and b are too disparate equation 8 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 The dual topology paradigm In a typical FEP setup involving the transformation 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 simula
13. carried out at the first timestep The reassignHold parameter may be set to limit the final temperature This parameter is valid only if reassignFreq has been set e reassignHold lt holding temperature for equilibration K gt Acceptable Values positive decimal Description The final temperature for reassignment when reassignIncr is set reassignTemp will be held at this value once it has been reached This parameter is valid only if reassignIncr has been set 6 4 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 6 6 9 6 4 1 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 61 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 sphericalBCCenter lt center of sphere A gt Acceptable Val
14. cellBasisVector1l 33 00 0 cellBasisVector2 0 32 0 0 cellBasisVector3 0 0 32 5 output params outputname tmp alanin binaryoutput no DcDfreq 10 restartfreq 100 integrator par timestep force field pa structure parameters exclude 1 4scaling switching switchdist cutoff pairlistdist stepspercycle ams 1 0 rams alanin psf alanin params scaled1 4 1 0 on 8 0 12 0 13 5 20 116 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 32 117 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
15. formed using PME the Ewald contribution should be estimated using a separate offline calculation based on the saved trajectory files The nonbonded contribution using a cutoff different from the one used in the simulation may also be computed offline in the same fashion as for Ewald if desired Pressure profile calculations may be performed in either constant volume or constant pressure conditions If constant pressure is enabled the slabs thickness will be rescaled along with the unit cell the dcdUnitCell option will also be switched on so that unit cell information is stored in the trajectory file NAMD 2 6 now reports the lateral pressure partitioned by interaction type Three groups are reported kinetic rigid bond restraints referred to as internal bonded and nonbonded If Ewald pressure profile calculations are active the Ewald contribution is reported in the nonbonded section and no other contributions are reported NAMD 2 6 also permits the pressure profile to be partitioned by atom type Up to 15 atom groups may be assigned and individual contribution of each group for the internal pressures and the pairwise contributions of interactions within and between groups for the nonbonded and bonded pressures are reported in the output file pressureProfile lt compute pressure profile gt Acceptable Values on or off Default Value off Description When active NAMD will compute kinetic bonded and nonbonded bu
16. 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 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 Basic Simulation Parameters 5 1 Non bonded interaction parameters and computations
17. posi ATOM kf KF ref X Y Z dist 2xATOM kf KF ref D angle 3x ATOM kf KF ref A dihe 4xATOM barr B ref A Bound Specifications not coupled to pmf calculations 85 posi bound ATOM kf KF low X Y Z D or hi X Y Z D dist bund 2x ATOM kf KF low D or hi D angle bound 3x ATOM kf KF low A or hi A dihe bound 4x ATOM gap E low A0 hi Al delta A2 Forcing Restraint Specifications coupled to pmf calculations posi pmf ATOM kf KF low X0 YO ZO hi X1 Y1 Z1 dist pmf 2xATOM kf KF low D0 hi D1 angle pmf 3x ATOM kf KF low A0 hi Al dihe pmf 4x ATOM barr B low A0 hi Al Units Input item Units E B kcal mol X Y Z D A degrees Ky kcal mol or kcal mol rad 6 7 4 Options for ATOM Specification The designation ATOM above stands for one of the following forms A single atom segname resnum atomname Example insulin 10 ca All atoms of a single residue segname resnum Example insulin 10 A list of atoms group segname resnum atomname segname resnum atomname Example group insulin 10 ca insulin 10 cb insulin 11 cg All atoms in a list of residues group segname resnum segname resnum Example group insulin 10 insulin 12 insulin 14 All atoms in a range of residues group segname resnum to segname resnum Example group insulin 10 to insulin 12 One or more atomnames in a list of residues
18. 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 sometimes reveal the origin of the instability 5 2 Full electrostatic integration 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 44 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 t
19. 72 MDLastStep parameter 73 MDOutputFreq parameter 73 topology psfgen command 35 TOTAL2 energy 23 TOTALS energy 23 twoAwayX 125 twoAwayY 125 twoAwayZ 125 T T T T T T T T units used for output 23 useConstantArea parameter 66 useConstantRatio parameter 66 useDPME parameter 53 useF lexibleCell parameter 66 useGroupPressure parameter 66 useSettle parameter 50 usMode parameter 97 vdwGeometricSigma parameter 49 velDCDfile parameter 22 velDCDfreq parameter 23 velocities parameter 20 velocityQuenching parameter 58 wrapAll parameter 65 wrapNearest parameter 65 wrapWater parameter 65 writepdb psfgen command 40 writepsf psfgen command 39 writeXiFreq parameter 97 xiMax parameter 95 xiMin parameter 95 XSTfile parameter 64 XSTfreq parameter 65 zeroMomentum parameter 49
20. Charm native communications layer and the program charmrun to launch namd2 processes for parallel runs either exclusively on the local machine with the local option or on other hosts as specified by a nodelist file The namd2 binaries for these platforms can also be run directly known as standalone mode for single process runs 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 MPT 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 9 1 Mac OS X Users Must Install the IBM XL C C Run Time Library The IBM XL C C compiler provides a significant performance boost to NAMD on PowerPC G4 and G5 processors Unfortunately the runtime library cannot be statically linked so you must download it from http ftp software ibm com aix products ccpp vacpp rte macos and install it based on the the README file in that directory If the library is not installed running NAMD will product this er
21. 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 53 5 3 7 Multiple timestep parameters 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 I or r RESPA method which is stable for timesteps up to 4 fs for long range electrostatic forces 2 fs for short range nonbonded forces and 1 fs for bonded forces Setting rigid all i e using SHAKE increases these timesteps to 6 fs 2 fs and 2 fs respectively but eliminates bond motion for hydrogen The mollified impulse method MOLLY reduces the resonance which limits the timesteps and thus increases these timesteps to 6 fs 2 fs and 1 fs while retaining all bond motion e fullElectFrequency lt number of timesteps between full electrostatic evaluations gt Acceptable Values positive integer factor of stepspercycle Default Value nonbondedFreq Description This parameter specifies the number of timesteps between each full elec trostatics evaluation It is recommended that fullElectFrequency be chosen so that the product of fullElectFrequency and timestep does not exceed 4 0 unless rigidBonds all or molly on is specified in which case the upper limit is perhaps doubled
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23. an output file basename and causes coor vel and xsc files to be written with that name e Between run commands the reassign Temp rescale Temp and langevinTemp parameters can be changed to allow simulated annealing protocols within a single config file The useGroup Pressure useFlexibleCell useConstantArea useConstantRatio LangevinPiston Langevin Piston Target LangevinPistonPeriod LangevinPistonDecay LangevinPistonTemp Surface Ten sion Target BerendsenPressure BerendsenPressureTarget BerendsenPressureCompressibil ity and BerendsenPressureRelaxationTime parameters may be changed to allow pressure equilibration The fixedAtoms constraintScaling and nonbondedScaling parameters may 16 be changed to preserve macromolecular conformation during minimization and equilibration fixed Atoms may only be disabled and requires that fixed AtomsForces is enabled 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 contai
24. and efficiency of PME For speed PMEGridSizeX should have only small integer factors 2 3 and 5 PMEGridSizeY lt number of grid points in y dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeY should have only small integer factors 2 3 and 5 PMEGridSizeZ lt number of grid points in z dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeZ should have only small integer factors 2 3 and 5 PMEProcessors lt processors for FFT and reciprocal sum gt Acceptable Values positive integer 52 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 FFTW 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 savi
25. and is an efficient full electrostatics method for use with periodic boundary conditions None of the parameters should affect energy conservation although they may affect the accuracy of the results and momentum conservation 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 10 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
26. be imposed on the distance between the centers of mass of residues 10 to 15 and residues 30 to 35 low 20 0 hi 10 0 indicates that the reference distance is 20 0at A 0 and 10 0at A 1 urestraint dist pmf group insulin 10 to insulin 15 group insulin 30 to insulin 35 kf 20 low 20 0 hi 10 0 1 during the initial 10 ps increase the strength of the forcing restraint to full strength 0 20 kcal mol 2 2 next apply a force to slowly close the distance from 20 to 10 A changes from 0 1 3 accumulate dU dA for another 10 ps stays fixed at 1 4 force the distance back to its initial value of 20 changes from 1 gt 0 pmf task grow time 10 ps print 1 ps pmf task up time 100 ps pmf task stop time 10 ps pmf task down time 100 ps 1 force the distance to close from 20 to 10 in 5 steps A changes from 0 1 0 2 0 4 0 6 0 8 1 0 at each step equilibrate for 10 ps then collect dU dA for another 10 ps ref 18 16 14 12 10 duration 10 10 x 5 100 ps FS 2a reverse the step above changes from 1 0 0 8 0 6 0 4 0 2 0 0 meti task stepup equiltime 10 ps accumtime 10 ps numsteps 5 print 1 ps meti task stepdown 89 6 7 7 Appendix Gradient for position restraint E Ky 2 7i Trefl E K5 2 2i tref Yi Yref zi zres V E
27. consForceFile parameter 70 consForceScaling parameter 70 conskcol parameter 56 conskfile parameter 56 consref parameter 56 constantForce parameter 69 constraints parameter 56 constraintScaling parameter 56 coord psfgen command 39 coordinate parameter 94 coordinates parameter 20 coordpdb psfgen command 39 coorfile command 17 129 cutoff parameter 45 cwd parameter 21 cylindricalBC parameter 63 cylindricalBCAxis parameter 63 cylindricalBCCenter parameter 63 cylindricalBCexp1 parameter 63 cylindricalBCexp2 parameter 64 cylindricalBCk1 parameter 63 cylindricalBCk2 parameter 64 cylindricalBC11 parameter 63 cylindricalBCl2 parameter 63 cylindricalBCr1 parameter 63 cylindricalBCr2 parameter 63 DCDfile parameter 22 DCDfreq parameter 22 DCDUnitCell parameter 22 delatom psfgen command 37 dielectric parameter 49 distFile parameter 97 dSmooth parameter 96 dxi parameter 95 eField parameter 70 eFieldOn parameter 70 error message Atoms moving too fast 44 Bad global exclusion count 44 exclude parameter 48 ExcludeFromPressure parameter 69 ExcludeFromPressureCol parameter 69 ExcludeFromPressureFile parameter 69 extCoordFilename parameter 82 extendedSystem parameter 64 extForceFilename parameter 82 extForces parameter 82 extForcesCommand parameter 82 fep parameter 102 fepCol parameter 103 fepEquilSteps parameter 103 fepFile parameter 103 fepOutFile parameter 103 fepOutFreq pa
28. e 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 excluded e 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 6 6 Applied Forces and Analysis There are several ways to apply external forces to simulations with NAMD These are described below 6 6 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 69 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 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 consfor
29. effect This parameter only has meaning if switching is set to on The value of switchdist must be less than or equal to the value of cutoff since the switching function is only applied on the range from switchdist to cutoff For a complete description of the non bonded force parameters see Section 5 1 e limitdist lt maximum distance between pairs for limiting interaction strength A gt Acceptable Values non negative decimal Default Value 0 Description The electrostatic and van der Waals potential functions diverge as the distance between two atoms approaches zero The potential for atoms closer than limitdist is instead treated as ar c with parameters chosen to match the force and potential at limitdist This option should primarily be useful for alchemical free energy perturbation calculations since it makes the process of creating and destroying atoms far less drastic energetically The larger the value of limitdist the more the maximum force between atoms will be reduced In order to not alter the other interactions in the simulation limitdist should be less than the closest approach of any non bonded pair of atoms 1 3 A appears to satisfy this for typical simulations but the user is encouraged to experiment There should be no performance impact from enabling this feature e pairlistdist lt distance between pairs for inclusion in pair lists A gt Acceptable Values positive decimal gt cutoff Default Value cutoff Descripti
30. 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 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 7 describes the relation between specific NAMD and X PLOR dynamics options Several sample NAMD configuration files are shown in section 8 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 spec
31. 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 remsh on HPUX is used to start namd2 on each node specified in the nodelist file You can change this via the CONV_RSH environment variable i e to use ssh instead of rsh run setenv CONV_RSH ssh or add it to your login or batch script You must be able to 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
32. frames were written every 1000 timesteps See Sec 6 11 for more about pair interaction calculations initial config coordinates alanin pdb temperature 0 output params outputname tmp alanin analyze binaryoutput no integrator params timestep 1 0 force field params structure alanin psf parameters alanin params exclude scaled1 4 1 4scaling 1 0 switching on switchdist 8 0 cutoff 12 0 pairlistdist 13 5 stepspercycle 20 Atoms in group 1 have a 1 in the B column group 2 has a 2 pairInteraction on pairInteractionFile pair pdb pairInteractionCol B pairInteractionGroup1 1 pairInteractionGroup2 2 First frame saved was frame 1000 set ts 1000 coorfile open dcd tmp alanin dcd Read all frames until nonzero is returned while coorfile read 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 0 118 incr ts 1000 coorfile close 119 9 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 if one is available For typical workstations Windows Linux Mac OS X or other Unix with only ethernet net working 100 Megabit or Gigabit NAMD uses the
33. from within the calcforces procedure For example loadcoords p and print p 4 e loadforces lt varname gt Loads the forces applied in the previous timestep in kcal mol Ao into a local array loadforces should only be called from within the calcforces procedure For example loadforces f and print f 4 e 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 e loadmasses lt varname gt Loads requested atom and group masses in amu into a local array loadmasses should only be called from within the calcforces procedure For example loadcoords m and print m 4 e addforce lt atomid groupid gt lt force vector gt Applies force in kcal mol 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 arti
34. group atomname segname resnum segname resnum group atomname atomname segname resnum segname resnum Examples group ca insulin 10 insulin 12 insulin 14 group ca cb cg insulin 10 insulin 12 insulin 14 group ca cb insulin 10 insulin 12 cg insulin 11 insulin 12 Note Within a group atomname is in effect until a new atomname is used or the keyword all is used atomname will not carry over from group to group This note applies to the paragraph below 86 One or more atomnames in a range of residues group atomname segname resnum to segname resnum group atomname atomname segname resnum to segname resnum Examples group ca insulin 10 to insulin 14 group ca cb cg insulin 10 to insulin 12 group ca cb insulin 10 to insulin 12 all insulin 13 6 7 5 Options for Potential of Mean Force Calculation The pmf and mcti blocks below are used to simultaneously control all forcing restraints specified in urestraint above These blocks are performed consecutively in the order they appear in the config file The pmf block is used to either a smoothly vary A from 0 1 or 1 0 or b set lambda The mcti block is used to vary from 0 1 or 1 0 in steps so that A is fixed while dU dX is accumulated Lamba control for slow growth pmf task up down stop grow fade or nog
35. minimizer gt Acceptable Values positive decimal Default Value 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 58 6 3 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 Temperature Control and Equilibration 6 3 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 7 although a different integrator is used langevin lt use Langevin dynamics gt Acceptable
36. non physical intermediate states or win dows 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 script is supplied at the end of this user guide The following keywords can be used to control the alchemical free energy calculations e fep lt Is alchemical FEP to be performed gt Acceptable Values on or off Default Value off Description Turns on hamiltonian scaling and ensemble averaging for alchemical FEP e lambda lt Coupling parameter value gt Acceptable Values positive decimal between 0 0 and 1 0 Description The coupling parameter value determining the progress of the perturba tion The non bonded interactions involving the atoms vanishing in the course of the MD simulation are scaled by 1 lambda while those of the growing atoms are scaled by lambda e lambda2 lt Coupling parameter comparison value 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 102 e fepEquilSteps lt Number of equilibration steps in a window before data collection gt Accep
37. 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 directory 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 121 group main pathfix tmp _mnt host alphal host alpha2 There are many other options to charmrun and for the nodelist file These are documented at in the Charm Installation and Usage Manual available at http charm cs uiuc edu manuals and a list of available charmrun options is available by running charmrun without arguments If your workstation cluster is controlled by a queueing system you will need build a nodelist file in your job script For example if your queueing system provides a HOST_FILE environment variable set NODES cat HOST_FILE set NODELIST TMPDIR namd2 nodelist echo group m
38. off the switching functions gend gewald PME on Use PME for electrostatic calculation Orthogonal periodic box size a 62 23 cellBasisVector1i 62 23 0 O b 62 23 cellBasisVector2 O 62 23 0 c 62 23 cellBasisVector3 O O 62 23 nfft1 64 PMEGridSizeX 64 nfft2 64 PMEGridSizeY 64 nfft3 64 PMEGridSizeZ 64 ischrgd 1 NAMD doesn t force neutralization of charge 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 a
39. 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 217 244 6078 Contents 1 Introduction 1 1 New features in version 2 6 e 1 2 NAMD and molecular dynamics simulations o e e 1 3 User feedback iii E a AA we a a Se SE BS KA i A
40. 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 also regenerate the patch grid In rare special circumstances atoms that are involved in bonded terms bonds angles dihedrals 43 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 to move in and out of the cutoff distance without causing energy conservation to be disturbed 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
41. same time You should probably determine the number of processors via a script for example on Scyld NUMPROCS bpstat u 1 charmrun namd2 p NUMPROCS lt configfile gt 122 You may safely suspend and resume a running NAMD job on these clusters using kill STOP and kill CONT on the process group Queueing systems typically provide this functionality allowing you to suspend a running job to allow a higher priority job to run immediately If you want to run multiple NAMD jobs simultaneously on the same cluster you can use the charmrun options startpe and endpe to specify the range of nodes to use The master node 1 is always included unless the skipmaster option is given The requested number of processes are assigned to nodes round robin as with other network versions or the ppn option can be used to specify the number of processes per node To limit the master node to one process use the singlemaster option 9 6 SGI Altix Be sure that the MPI_DSM_DISTRIBUTE environment variable is set then use the Linux ia64 MPT version of NAMD along with the system mpirun mpirun np lt procs gt lt configfile gt 9 7 Compaq AlphaServer SC If your machine as a Quadrics interconnect you should use the Elan version of NAMD other wise select the normal MPI version In either case parallel jobs are run using the prun command as follows prun n lt procs gt lt configfile gt There are additional options Consul
42. then no harmonic constraints are computed If it is set to on then harmonic constraints are calculated using the values specified by the parameters consref conskfile conskcol and consexp e consexp lt exponent for harmonic constraint energy function gt Acceptable Values positive even integer Default Value 2 Description Exponent to be use in the harmonic constraint energy function This value must be a positive integer and only even values really make sense This parameter is used only if constraints is set to on e consref lt PDB file containing constraint reference positions gt Acceptable Values UNIX file name Description PDB file to use for reference positions for harmonic constraints Each atom that has an active constraint will be constrained about the position specified in this file e conskfile lt PDB file containing force constant values gt Acceptable Values UNIX filename Description PDB file to use for force constants for harmonic constraints e conskcol lt column of PDB file containing force constant gt Acceptable Values X Y Z 0 or B Description Column of the PDB file to use for the harmonic constraint force constant This parameter may specify any of the floating point fields of the PDB file either X Y Z occupancy or beta coupling temperature coupling Regardless of which column is used a value of 0 indicates that the atom should not be constrained Otherwise the value specified is used as th
43. times 6 Read protein coordinates from PDB file The same file used to generate the sequence is now read to extract coordinates In the residue ILE the atom CD is called CD1 in the pdb file so we use pdbalias atom to define the correct name If the segment names in the pdb file match the name we gave in the segment statement then we don t need to specify it again in this case we do specify the segment so that all atoms in the pdb file must belong to the segment 7 Build water segment Build a segment for the crystal waters The residue type for 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 mi
44. to contain the protein For more information on how atomselections can be used within VMD scripts see the VMD User s Guide proc addwater psffile pdbfile watpsf watpdb Create psf pdb files that contain both our protein as well as a box of equilibrated water The water box should be large enough to easily contain our protein resetpsf readpsf psffile 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 struc
45. 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 SMDDir SMD thus results in the following potential being applied to the system 1 U ri T2 t 5 k vt RE Ro ai 3 Here t Ni dt where Nts is the number of elapsed timesteps in the simulation and dt is the size of the timestep in femtoseconds Also R t is the current center of mass of the SMD atoms and Ro is the initial center of mass as defined by the coordinates in SMDFile Vector is normalized by NAMD before being used Output NAMD provides output of the current SMD data The frequency of output is specified by the SMDOutputFreq parameter in the configuration file Every SMDOutputFreq timesteps NAMD will print the current timestep current position of the center of mass of the restrained atoms and the current force applied to the center of mass in piconewtons pN The output line starts with word SMD 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
46. use for the containing fixed atom parameters for each atom The coefficients can be read from any floating point column of the PDB file A value of 0 indicates that the atom is not fixed 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 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
47. use the NAMD Tcl scripting interface as described in Sec 2 2 2 to run for O steps so that NAMD prints the energy without performing any dynamics e pairInteraction lt is pair interaction calculation active gt Acceptable Values on or off Default Value off Description Specifies whether pair interaction calculation is active e pairInteractionFile lt PDB file containing pair interaction flags gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to specify atoms to use for pair interaction calculations If this parameter is not specified then the PDB file containing initial coordinates specified by coordinates is used e pairInteractionCol lt column of PDB file containing pair interaction flags gt Acceptable Values X Y Z 0 or B Default Value B Description Column of the PDB file to specify which atoms to use for pair interaction calculations This parameter may specify any of the floating point fields of the PDB file either X Y Z occupancy or beta coupling temperature coupling e pairInteractionSelf lt compute within group interactions instead of bewteen groups gt Acceptable Values on or off Default Value off Description When active NAMD will compute bonded and nonbonded interactions only for atoms within group 1 e pairInteractionGroupi lt Flag to indicate atoms in group 1 gt Acceptable Values integer Description e pairInteractionGroup2 lt Flag to indicate a
48. 00 000 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 9 11 Improving Parallel Scaling While NAMD is designed to be a scalable program particularly for simulations of 100 000 atoms or more at some point adding additional processors to a simulation will provide little or no extra performance If you are lucky enough to have access to a parallel machine you should measure NAMD s parallel speedup for a variety of processor counts when running your particular simulation The easiest and most accurate way to do this is to look at the Benchmark time lines that are printed after 20 and 25 cycles usually less than 500 steps You can monitor performance during the entire simulation by adding outputTiming steps to your configuration file but be careful to look at the wall time rather than CPU time fields on the TIMING output line
49. 10 1 Structure Generation To use LES the structure and coordinate input files must be modified to contain multiple copies of the enhanced atoms psfgen provides the multiply command for this purpose NAMD supports a maximum of 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 6 10 2 Simulation In practice LES is a simple method used to increase sampling no special output is generated The following parame
50. 2 parameter is encountered in PARM file NAMD will terminate 3 NAMD has several exclusion policy options defined by exclude The way AMBER dealing with exclusions corresponds to the scaled1 4 in NAMD So for simulations using AMBER force field one would specify exclude scaled1 4 in the configuration file and set 1 4scaling to the inverse value of SCEE as would be used in AMBER 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
51. 28 39 2004 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 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 D Rodriguez Gomez E Darve and A Pohorille Assessing the efficiency of free energy calculation methods J Chem Phys 120 3563 3578 2004 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 95 9277 9287 1991 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 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 CMTT 1 122 35 8392 8402 2000 M Sprik and G Cicotti Free energy from constrained molecular dynamics J Chem Phys 109 7737 7744 1998 T P Straatsma an
52. ABF simulations The formalism implemented in NAMD had been originally devised in the framework of uncon strained MD Holonomic constraints may however be introduced without interfering with the computation of the bias and hence the PMF granted that some precautions are taken Either of the following strategies may be adopted 1 Atoms involved in the computation of F do not participate in constrained degrees of freedom E If for instance chemical bonds between hydrogen and heavy atoms are frozen could be chosen as a distance between atoms that are not involved in a constraint In some cases not all atoms used for defining are involved in the computation of the force component Fg Specifically reference atoms abf1 in the RC types zCoord and zCoord 1atom are not taken into account in Fg Therefore constraints involving those atoms have no effect on the ABF protocol 2 The definition of involves atoms forming constrained bonds In this case the effect of constraints on ABF can be eliminated by using a group based RC built on atom groups containing both ends of all rigid bonds involved e hydrogens together with their mother atom For example if the distance from a methane molecule to the center of mass of a water lamella is studied with the zCoord RC by taking water oxygens as a reference abf1 and all five atoms of methane as the group of interest abf2 e Water molecules may be constrained because the r
53. 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 Restart file frequency ntwx 100 DCDfreq 100 Trajectory file frequency dt 0 001 timestep 1 in unit of fs This is default tempi 0 temperature O Initial temp for velocity assignment cut 10 cutoff 10 switching off Turn off the switching functions scee 1 2 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
54. BER format PARM file gt Acceptable Values UNIX filename Description This file contains complete topology and parameter information of the system e ambercoor lt AMBER format coordinate file gt Acceptable Values UNIX filename Description This file contains the coordinates of all the atoms Note that coordinates can also be used for PDB format coordinate file When amber is set to on either ambercoor or coordinates must be defined but not both e readexclusions lt Read exclusions from PARM file gt Acceptable Values yes or no Default Value 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 1
55. MD should scale very well when the number of patches multiply the dimensions of the patch grid is larger or rougly the same as the number of processors If this is not the case it may be possible to improve scaling by adding twoAwayX yes to the config file which roughly doubles the number of patches Similar options twoAwayY and twoAwayZ also exist and may be used in combination but this greatly increases the number of compute objects twoAwayX has the unique advantage of also improving the scalability of PME 125 10 NAMD Availability and Installation NAMD is distributed freely for non profit use NAMD 2 6 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 6 10 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 10 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 6 binaries are available for the following platforms e Windows NT etc on x86 processors e Mac OS X also called Darwin on PowerPC and Int
56. MD supports CHARMM19 CHARMM22 and CHARMM27 parameter files in both X PLOR and CHARMM formats X PLOR format is the default CHARMM format parameter files may be used given the parameter paraTypeCharmm on For a full description of the format of commands used in these files see the X PLOR and CHARMM User s Manual 7 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 parame
57. Mass parameter 106 lesReduceTemp parameter 106 limitdist parameter 46 longSplitting parameter 54 margin parameter 47 margin violations 43 maximumMove parameter 59 measure command 17 mergeCrossterms parameter 23 minBabyStep parameter 58 minimization parameter 58 minimize command 16 minLineGoal parameter 58 minTinyStep parameter 58 MISC energy 23 molly parameter 55 mollyIterations parameter 55 mollyTolerance parameter 55 moveBoundary parameter 97 movingConstraints parameter 71 movingConsVel parameter 71 MTSAlgorithm parameter 54 multiply psfgen command 37 mutate psfgen command 37 nonbondedFreq parameter 54 nonbondedScaling parameter 49 numsteps parameter 45 OPLS 49 outFile parameter 96 output command 16 outputEnergies parameter 23 outputFreq parameter 96 outputMomenta parameter 23 outputname parameter 21 outputPairlists parameter 47 outputPressure parameter 23 outputTiming parameter 24 pairInteraction parameter 107 pairInteractionCol parameter 107 pairInteractionFile parameter 107 pairInteractionGroupl1 parameter 107 pairInteractionGroup2 parameter 107 pairInteractionSelf parameter 107 pairlistdist parameter 46 pairlistGrow parameter 48 pairlist MinProcs parameter 47 pairlistShrink parameter 47 pairlistsPerCycle parameter 47 pairlist Trigger parameter 48 parameters parameter 20 paraTypeCharmm parameter 20 paraTypeXplor parameter 20 parmfile parameter 24 patc
58. 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 New features in version 2 6 Ports to Itanium Altix and Opteron Athlon64 EMT64 NAMD runs very fast on the Itanium processor under Linux including the SGI Altix Native binaries for 64 bit x86 processors such as AMD Opteron and Intel EMT64 are 25 faster than 32 bit binaries Port to Mac OS X for Intel Processors NAMD has been ported to the new Intel based Macintosh platform Binaries are only 32 bit but should run on newer 64 bit machines Ports to Cray XT3 and IBM BlueGene L source code only These two large scalable but immature platforms are now supported Neither platform supports dynamic linking and our experience shows that binaries would be quickly out of date so only source code is released Also BlueGene L requires the latest development version of Charm rather than charm 5 9 as shipped with the NAMD source code 10 Improved Serial Performance Especially on POWER and PowerPC Tuning of the NAMD inner loop has provided a 30 performance boost with the IBM XL compiler New Mac OS X binaries are up to 70 faster but users must download the IBM XL runtime library from http ftp software ibm com aix products ccpp vacpp rte macos Adaptive Biasing Force Free Energy Calculations A new method impl
59. 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 1 1 Non bonded 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 switchdist cutoff De a AAA Gp AAAS Sat energy T I I I I I distance Figure 1 Graph of van der Waals potential with and without the application of the switching function With the switching function active the potential is smoothly reduced to 0 at the cutoff distance Without the switching function there is a discontinuity where the potential is truncated The switching function used is based on the X PLOR switching function The parameter switchdist specifies the distance at which t
60. RAJectory Filename for the position trajectory file NAMD Parameter DCDfreq X PLOR Parameter NSAVC Number of timesteps between writing coordinates to the trajectory file NAMD Parameter velDCDfile X PLOR Parameter VELOcity Filename for the velocity trajectory file NAMD Parameter velDCDfreq X PLOR Parameter NSAVV Number of timesteps between writing velocities to the trajectory file NAMD Parameter numsteps X PLOR Parameter NSTEp Number of simulation timesteps to perform 114 8 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 20 115 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
61. 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 Description 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 74 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 Va
62. TI_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 protein segment patch DISU BPTI 5 BPTI 55 patch DISU BPTI 14 BPTI 38 patch DISU BPTI 30 BPTI 51 6 Read protein coordinates from PDB file pdbalias atom ILE CD1 CD formerly alias atom coordpdb output 6PTI_protein pdb BPTI 7 Build water segment 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 thi
63. TMDk lt Elastic constant for TMD forces gt Acceptable Values Positive value in kcal mol A Description The value of k in Eq 2 A value of 200 seems to work well in many cases 72 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 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 in this file Non targeted atoms are ignored TMDFirstStep lt first TMD timestep gt Acceptable Values Positive integer Default Value 0 Description TMDLastStep lt last TMD timestep gt Acceptable Values Positive integer Description TMD forces are applied only between TMDFirstStep and TMDLastStep The target RMSD evolves linearly in time from the initial to the final target value TMDInitialRMSD lt target RMSD at first TMD step gt Acceptable Values Non negative value in A Default Value from coordinates Description In order to perform TMD calculations that involve restarting a previous NAMD run be sure to specify TMDInitia
64. This file contains a history of the information stored in outFile and is written every tenth update of outFile Data for different timesteps are separated by amp signs for easier visualization using the Grace plotting software This is useful for assessing the convergence of the free energy profile inFiles lt Input files for an ABF calculation gt Acceptable Values Tcl list of Unix filenames Default Value empty list Description Input files containing the same data as in outFileName and that may therefore be used to restart an ABF simulation The new free energies and forces will then be written out based on the original information supplied by these files This command may also be used to combine data obtained from separate runs outputFreq lt Frequency at which outFileName is updated gt Acceptable Values positive integer Default Value 5000 Description The free energy A the average force F and the number of samples accrued in the bin will be written to the ABF output file every ABFoutFreq timesteps 96 writeXiFreq lt Frequency at which the time series of is written gt Acceptable Values positive integer Default Value 0 Description If this parameter is nonzero the instantaneous value of the reaction coordi nate is written in the NAMD standard output every writeXiFreq time steps distFile lt Output file containing force distributions gt Acceptable Values Unix filename Default Va
65. Values on or off Default Value off Description Specifies whether or not Langevin dynamics active If set to on then the parameter langevinTemp must be set and the parameters langevinFile and langevinCol can optionally be set to control the behavior of this feature 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 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 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 langevinFile lt PDB file containing Langevin parameters gt Acceptable Values UNIX filename Default Value coord
66. a molecule crosses a periodic boundary it is not translated to the other side of the cell on output This option alters this behavior for all contiguous clusters of bonded atoms e wrapNearest lt use nearest image to cell origin when wrapping coordinates gt Acceptable Values on or off Default Value off Description Coordinates are normally wrapped to the diagonal unit cell centered on the origin This option combined with wrapWater or wrapA11 wraps coordinates to the nearest image to the origin providing hexagonal or other cell shapes 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
67. able Values on or off Default Value off Description Restrain the Cartesian z components of the positions 6 1 2 Fixed atoms parameters Atoms may be held fixed during a simulation NAMD avoids calculating most interactions in which all affected atoms are fixed unless fixedAtomsForces is specified e fixedAtoms lt are there fixed atoms gt Acceptable Values on or off Default Value off Description Specifies whether or not fixed atoms are present e fixedAtomsForces lt are forces between fixed atoms calculated gt Acceptable Values on or off Default Value off Description Specifies whether or not forces between fixed atoms are calculated This option is required to turn fixed atoms off in the middle of a simulation These forces will affect the pressure calculation and you should leave this option off when using constant pressure if the coordinates of the fixed atoms have not been minimized The use of constant pressure with significant numbers of fixed atoms is not recommended 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 57 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
68. ading CHARMM topology files e reading psf files in X PLOR NAMD format e extracting sequence data from single segment PDB files e generating a full molecular structure from sequence data e applying patches to modify or link different segments e writing NAMD and VMD compatible PSF structure files e extracting coordinate data from PDB files e constructing guessing missing atomic coordinates e deleting selected atoms from the structure e writing NAMD and VMD compatible PDB coordinate files We are currently refining the interface of psfgen and adding 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 Ge
69. 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 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 distr
70. ain 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 9 4 Windows Workstation Networks Windows is the same as other workstation networks described above except that rsh is not available on this platform Instead you must run the provided daemon charmd exe on every node listed in the nodelist file Using charmd_faceless rather than charmd will eliminate consoles for the daemon and node processes 9 5 BProc Based Clusters Scyld and Clustermatic Scyld and Clustermatic replace rsh and other methods of launching jobs via a distributed process space There is no need for a nodelist file or any special daemons although special Scyld or Clustermatic versions of charmrun and namd2 are required In order to allow access to files the first NAMD process must be on the master node of the cluster Launch jobs from the master node of the cluster via the command charmrun namd2 p lt procs gt lt configfile gt For best performance run a single NAMD job on all available nodes and never run multiple NAMD jobs at the
71. akes the coordinates of the three atoms as input and returns a list of 1 fe 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 r 73 74 in radian This command takes the coordinates of the four atoms as input and returns a list of 1 oe oe oe Each element of the list is a 3 D vector in the form of a Tcl list 2 T3 TA 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 dihedral set aidi 112 set aid2 123 set aid3 117 set aid4 115 The spring constant for the harmonic constraint set k 3 0 addatom aid1 addatom aid2 addatom aid3 addatom aid4 set PI 3 1416 proc calcforces global aidi aid2 aid3 aid4 k PI loadcoords p Calculate the current dihedral set phi getdihedral p aid1 p aid2 p aid3 p aid4 Change to radian set phi expr phi PI 180 optional Add this constraining energy to MISC in the energy output addenergy expr k phi phi 2 0 78 Calculate the force along the dihedral according to the harmonic constraint set fo
72. ance 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 determine the minimum patch size Unless the splitPatch parameter is explicitly set to position hydrogen atoms will be placed on the same patch as the mother atom to which they are bonded These hydrogen groups are then distance tested against each other using only a cutoff increased by the the value of the hgroupCutoff parameter The size of the patches is also increased by this amount NAMD functions correctly even if a hydrogen atom and its mother atom are separated by more than half of hgroupCutoff by breaking that group into its individual atoms for distance testing Margin violation warning messages are printed if an atom moves outside of a safe zone surrounding the patch to which it is assigned indicating that pairlistdist should be increased in order for forces to be calculated correctly and energy to be conserved Margin violations mean that atoms that are in non neighboring patches may be closer than the cutoff distance apart This may sometimes happen in constant pressure simulations when the cell shrinks since the
73. angevin dynamics do not conserve momentum use in combination with these features should be considered experimental Since the momentum correction is delayed enabling outputMomenta will show a slight nonzero linear momentum but there should be no center of mass drift 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 or no Defa
74. atics Algorithms NAMD incorporates the Particle Mesh Ewald PME algorithm which takes the full elec trostatic interactions into account This algorithm reduces the computational complexity of electrostatic force evaluation from O N to O N log N e Multiple Time Stepping The velocity Verlet integration method 1 is used to advance the positions and velocities of the atoms in time To further reduce the cost of the evaluation of long range electrostatic forces a multiple time step scheme is employed The local interactions bonded van der Waals and electrostatic interactions within a specified distance are calculated at each time step The longer range interactions electrostatic interactions beyond the specified distance are only computed less often This amortizes the cost of computing the electrostatic forces over several timesteps A smooth splitting function is used to separate a quickly varying short range portion of the electrostatic interaction from a more slowly varying long range component It is also possible to employ an intermediate timestep for the short range non bonded interactions performing only bonded interactions every timestep e Input and Output Compatibility The input and output file formats used by NAMD are identical to those used by CHARMM and X PLOR Input formats include coordinate files in PDB format 3 structure files in X PLOR PSF format and energy parameter files in either CHARMM or X PLOR formats Output fo
75. bonded interaction parameters and computations 5 1 1 Non bonded van der Waals interactions 2 20 4 5 1 2 Non bonded electrostatic interactions 2 2 00 4 5 1 3 Nonbonded interaction distance testing o e a 5 2 Full electrostatic integration 2 e 5 3 NAMD configuration parameters ooo 5 3 1 Timestep parameters e e 5 3 2 Simulation space partitioning e 5 3 3 Basic dynamics os C 24468 a a a e a a e a a a ee 10 10 11 13 14 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 3 4 DPMTA parameters n an p e a a a a a 50 5 3 5 PME parameters eona i a E a Ea e E E e e S 52 5 3 6 Full direct parameters e 53 5 3 7 Multiple timestep parameters 2 54 6 Additional Simulation Parameters 56 6 1 Constraints and Restraints e 56 6 1 1 Harmonic constraint parameters a 56 6 1 2 Fixed atoms parameters 57 6 2 Energy Minimization aoaaa e 58 6 2 1 Conjugate gradient parameters oo a a 58 6 2 2 Velocity quenching parameters a 58 6 3 Temperature Control and Equilibration o oo e e 59 6 3 1 Langevin dynamics parameters a 59 6 3 2 Temperature coupling parameters a 60 6 3 3 Temperature rescaling parameters a 60 6 3 4 Temperature reassignment parameters soosoo e e e a 61 6 4 Boundary Conditio
76. 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 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
77. cefile is optional constant forces may be specifed 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 6 6 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 6 6 3 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 F t
78. ceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect along the cylinder axis cylindricalBCk1 lt force constant for first potential gt Acceptable Values non zero decimal Description Force constant for the first harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center cylindricalBCexp1 lt exponent for first potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for first boundary potential The only likely values to use are 2 and 4 cylindricalBCr2 lt radius for 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 63 e cylindricalBCk2 lt force constant for second potential gt Acceptable Values non zero decimal Description Force constant for the second harmonic potential A positive value wi
79. cheme the cutoff parameter has a slightly different meaning 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 5 2 direct at gt E every step o cutoff 0 t 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 42 5 1 3 Nonbonded 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
80. cknowledgements ss tia pe ep A GL ek ee eee Re ey kam da Getting Started 2 1 What is needed 2 2 2 2 200 12 2 ee pa a eee ana 2 2 NAMD configuration fle si 4h eo pede EME Poe A ete a Ge oe e 2 2 1 Configuration parameter syntax 2 0 ee ee 2 2 2 Tcl scripting interface and features 2 2 0 0 o 2 2 3 Required NAMD configuration parameters 28 4 Input and Output Files 3 1 Fille formats our AR eek BG Ee a we a aA Qala POB A hy eons SESS pe de e Beth ok ee BS 3 12 X PLOR format PSE files os e ecg gS ae e as Rey ia 3 1 3 CHARMM19 CHARMM22 and CHARMM27 parameter files 3 L4 DCD trajectory files stak o 6 ei ee ew ea ee ee ee 3 2 NAMD configuration parameters 2 0 ee ee B22 A gt Tpit files ene e Soke Re nary Re Ce a ee a eee nh ee ae 3 2 2 Qutput files mi ee ee ba eee RE Ee wee eee ad 3 2 3 Standard output spa a egos lg Bee ee et eee a es 3 3 AMBER force field parameters 2 2 0 ee ee 3 4 GROMACS force field parameters 0002 eee ee ees Creating PSF Structure Files AN Ordinary Usage a qo Rb ao ee Pa es lg tee Oe Sec A a 4 1 1 Preparing separate PDB files 0 o 4 1 2 Deleting unwanted atoms 0000 eee ee 42 BPTI Example A 4 4 oN A A 1 A a ett a e a 4 3 Building solvent around a protein osoa ee AA Listrof Commands oros cy ote Pears A ag ee Oe BS 4 5 Example of a Session Log 1 eu n Dap ia a ee Basic Simulation Parameters 5 1 Non
81. command At this point only pure Tcl syntax is allowed In addition the idiom for Tcl comments will only work with Tcl enabled NAMD has also traditionally allowed parameters to be specified as param value This is supported but only before the first run command Some examples this is my config file lt OK reassignFreq 100 how often to reset velocities lt only w Tcl reassignTemp 20 temp to reset velocities to lt OK before run run 1000 lt now Tcl only reassignTemp 40 temp to reset velocities to lt is required NAMD has also traditionally allowed parameters to be specified as 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 45 e coordinates page 20 e structure page 20 e parameters page 20 e exclude page 48 e outputname page 21 e one of the following three temperature page 48 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 package
82. ction 6 6 4 Rotating Constraints The constraints parameters are specified in the same manner as for usual static harmonic con straints The reference positions of all constrained atoms are then rotated with a given angular velocity about a given axis If the force constant of the constraints is sufficiently large the con strained atoms will follow their reference positions A rotation matrix M about the axis unit vector v is calculated every timestep for the angle of rotation corresponding to the current timestep angle Qt where Q is the angular velocity of rotation From now on all quantities are 3D vectors except the matrix M and the force constant K The current reference position R is calculated from the initial reference position Ry at t 0 R M Ro P P where P is the pivot point Coordinates of point N can be found as N P R P v v Normal from the atom pos to the axis is similarly normal P X P v v X The force is as usual F K R X This is the force applied to the atom in NAMD see below NAMD does not know anything about the torque 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 wil
83. d J A McCammon Computational alchemy Annu Rev Phys Chem 43 407 435 1992 G M Torrie and J P Valleau Nonphysical sampling distributions in monte carlo free energy estimation Umbrella sampling J Comput Phys 23 187 199 1977 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 R W Zwanzig High temperature equation of state by a perturbation method i nonpolar gases J Chem Phys 22 1420 1426 1954 128 Index 1 4scaling parameter 49 abf command 94 alias psfgen command 35 39 amber parameter 24 ambercoor parameter 24 applyBias parameter 97 Atoms moving too fast 44 auto psfgen command 36 Bad global exclusion count 44 BerendsenPressure parameter 66 BerendsenPressureCompressibility parameter 67 BerendsenPressureFreq parameter 67 BerendsenPressureRelaxationTime parameter 67 BerendsenPressureTarget parameter 67 binaryoutput parameter 21 binaryrestart parameter 22 bincoordinates parameter 21 binvelocities parameter 21 BOUNDARY energy 23 callback command 16 cellBasisVectorl parameter 64 cellBasisVector2 parameter 64 cellBasisVector3 parameter 64 cellOrigin parameter 64 checkpoint command 17 COMmotion parameter 48 consexp parameter 56
84. d in pairs to set a lower and upper bound Torsional bounds always are defined in pairs 6 7 2 Free Energy Calculations Conformational forcing Potential of mean force In conformational forcing calculations structural parameters such as atomic positions inter atomic distances and dihedral angles are forced to change by application of changing restraint potentials For example the distance between two atoms can be restrained by a potential to a 84 mean distance that is varied during the calculation The free energy change or potential of mean force pmf for the process can be estimated during the simulation The potential is made to depend on a coupling parameter A whose value changes during the simulation In potential of mean force calculations the reference value of the restraint potential depends on A Alternately the force constant for the restraint potential may change in proportion to the coupling parameter Such a calculation gives the value of a restraint free energy i e the free energy change of the system due to imposition of the restraint potential Methods for computing the free energy With conformational forcing or with molecular transformation calculations one obtains a free energy difference for a process that is forced on the system by changing the potential energy function that determines the dynamics of the system One always makes the changing potential depend on a coupling parameter A By convention ca
85. dihedral angle restraint E E0o 2 1 COS xi a Xref Atoms at positions A B C D ALAS eee CDxCB BCxBA Xi cos u cos cB cB AND BCxBA Xi sin v sin CDxCB x BCxBA TB papa e 90 V E Eo0 2 sin xi Xref V xai V xi Fe V u CDxCB yp yc 2n 2c 20 2c ya ya Y zp 2c tB zc up 2c 2B 20 J tp zc ye yc yp yc 2s 2c k pit poj p3k BC x BA yo ys za 28 zo zB ya ym 2c 2B a ZB c tB ZA 28 zo TB YA YB yo yB tA amp B k psi psj pek u Pips t paps Pape V Pi tps p Pi tps p pr pa 2 Nips SDs vips vy V Pit P53 P3 Y PG D5 Dg E ea 1 2 03 p3 pg 2pa V pa 2ps V ps 2p6 V pe o a 1 2 p p3 p3 9 2p1 V p1 2p2 V p2 2p3 V ps for atom A moving atoms B C amp D fixed V p1 0 0 0 0 7 0 0 k V p2 ia 0 0 7 0 0 k V p3 0 0 i 0 0 7 0 0 F V pa 0 0 zp zc F yo yB k V ps 20 zp t 0 0 7 2B z0 k Vips ye yc i tc 1B j 0 0 k for atom B moving atoms A C amp D fixed V p1 0 0 P zeo zp F yo yc F V p2 2p 20 1 0 0 7 20 2D k V ps yo yp it xzp zrc f 0 0 V pa 0 0 P 2e za F ya yo F V ps 24 20 1 0 0 F u0
86. e binaryrestart or binaryoutput options Note that in the current implementation at least the bincoordinates option must be used in addition to the coordinates option but the positions specified by coordinates will then be ignored e cwd lt default directory gt Acceptable Values UNIX directory name Description The default directory for input and output files If a value is given all filenames that do not begin with a are assumed to be in this directory For example if cwd is set to scr 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 binar
87. e energy from molecular dynamics with multiple con straints Mol Phys 98 773 781 2000 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 J H nin and C Chipot Overcoming free energy barriers using unconstrained molecular dynamics simulations J Chem Phys 121 2904 2914 2004 W Humphrey and A Dalke VMD user guide Version 0 94 Beckman Institute Technical Report TB 94 07 University of Illinois 1994 127 17 18 19 20 21 22 23 24 25 28 29 30 31 32 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 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
88. e force constant for that atom s restraining potential e constraintScaling lt scaling factor for harmonic constraint energy function gt Acceptable Values positive Default Value 1 0 Description The harmonic constraint energy function is multiplied by this parameter making it possible to gradually turn off constraints during equilibration This parameter is used only if constraints is set to on 56 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 Accept
89. earance The format of the free energy perturbation script is described below The following sections describe the format of the free energy perturbation script 6 7 1 User Supplied Conformational Restraints These restraints extend the scope of the available restraints beyond that provided by the harmonic position restraints Each restraint is imposed with a potential energy term whose form depends on the type of the restraint Fixed Restraints Position restraint 1 atom force constant Kp and reference position Tref E Ky 2 Ti ref Stretch restraint 2 atoms force constant Ky and reference distance dref E K5 2 di def Bend restraint 3 atoms force constant Kp and reference angle Ores E Ky 2 0 ref Torsion restraint 4 atoms energy barrier Eo and reference angle Xref BS Eo 2 1 COS Xi Xref Forcing restraints Position restraint 1 atom force constant Kp and two reference positions 76 and T E Ky 2 U T Pref ATI 1 A T Stretch restraint 2 atoms force constant Kp and two reference distances do and di E Ky 2 di dref dref di 1 A do Bend restraint 3 atoms force constant Kp and two reference angles 6o and 01 E K5 2 0 reg Ores M1 1 A Oo Torsion restraint 4 atoms energy barrier Eo and two reference angles xy and x1 E Eo 2 1 cos Xi Xref Xref AX 1 A XO 83 The forcing restraints depend on the coupl
90. easonable number of force samples has been collected When the user defined minimum number of samples is reached the biasing force is introduced progressively in the form of a linear ramp For optimal efficiency this minimal number of samples should be adjusted on a system dependent basis In addition to alleviate the deleterious effects caused by abrupt variations of the force the corresponding fluctuations are smoothed out using a weighted running average over a preset number of adjacent bins in lieu of the average of the current bin itself It is however crucial to ascertain that the free energy profile varies regularly in the interval over which the average is performed To obtain an adequate sampling in reasonable simulation times it is recommended to split long reaction pathways into consecutive ranges of In contrast with probability based methods ABF does not require that these windows overlap by virtue of the continuity of the force across the the reaction pathway A more comprehensive discussion of the theoretical basis of the method and its implementation in NAMD can be found in 15 6 8 2 Using the NAMD implementation of the adaptive biasing force method The ABF method has been implemented as a suite of Tcl routines that can be invoked from the main configuration file used to run molecular dynamics simulations with NAMD 93 The routines can be invoked by including the following command in the configuration file
91. ee 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 commercial use of the Software Licensee will contact Illinois namd ks uiuc edu to negotiate an appropriate license for such use Commercial use includes 1 integration of all or part of the Software into a product for sale lease
92. eference atoms are not used to compute the force component e C H bonds in methane may be constrained as well because the contributions of constraint forces on the carbon and hydrogens to F will cancel out 6 8 6 Example of input file for computing potentials of mean force In this example the system consists of a short ten residue peptide formed by L alanine amino acids Reversible folding unfolding of this peptide is carried out using as a reaction coordinate the carbon atom of the first and the last carbonyl groups hence corresponds to a a simple interatomic distance defined by the keyword distance The reaction pathway is explored between 12 and 32 A i e over a distance of 20 A in a single window The variations of the free energy derivative are soft enough to warrant the use of bins with a width of 0 2 A in which forces are accrued source lib abf abf tcl abf coordinate distance abf abfi 4 abf abf2 99 abf dxi 0 2 abf xiMin 12 0 99 abf xiMax 32 0 abf outFile deca alanine dat abf fullSamples 500 abf inFiles abf distFile deca alanine dist abf dSmooth 0 4 Here the ABF is applied after 500 samples have been collected which in vacuum have proven to be sufficient to get a reasonable estimate of F 6 9 Alchemical Free Energy Perturbation Calculations This feature has been contributed to NAMD by the following authors Surjit B Dixit J r me H nin and Christophe Chipot Equipe de dynam
93. efinition 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 sequence 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
94. eger Default Value 2 Description Exponent for second boundary potential The only likely values to use are 2 and 4 6 4 2 Cylindrical harmonic boundary conditions NAMD provides cylindrical harmonic boundary conditions These boundary conditions can consist of a single potential or a combination of two potentials The following parameters are used to define these boundary conditions 62 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 cylindricalBCl1 and cylindricalBCk1 must be defined and cylindricalBCAxis cylindricalBCexp1 cylindricalBCr2 cylindricalBC12 cylindricalBCk2 and cylindricalBCexp2 can optionally be defined cylindricalBCCenter lt center of cylinder A gt Acceptable Values position Description Location around which cylinder is centered cylindricalBCAxis lt axis of cylinder A gt Acceptable Values x y or z Description Axis along which cylinder is aligned cylindricalBCr1 lt radius for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect along the non axis plane of the cylinder cylindricalBCl1 lt distance along cylinder axis for first boundary condition A gt Ac
95. el processors e AIX on POWER processors with and without MPI e Linux on x86 x86 64 AMD64 EMT64 and Itanium 1A64 processors e Scyld Beowulf on x86 processors e Clustermatic 4 5 on x86 processors e Solaris on Sparc processors with and without MPI e Tru64 Unix on Alpha processors with and without MPI e Compaq AlphaServer SC using the Quadrics Elan library e SGI Origin 2000 with and without MPI e SGI Altix with MPI 10 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 10 4 Documentation All available NAMD documentation is available for download without registration via the NAMD web site http www ks uiuc edu Research namd 126 References 1 10 11 12 13 14 15 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 F C Berns
96. emented in Tcl efficiently calculates the potential of mean force along a reaction coordinate by applying adaptive biasing forces to provide uniform sampling Customizable Replica Exchange Simulations The replica exchange method is implemented as a set of Tcl scripts that use socket connections to drive a set of NAMD jobs exchanging temperatures or any other scriptable parameter based on energy Tcl Based Boundary Potentials Tcl scripted forces may be efficiently applied individually to large numbers of atoms to implement boundaries and similar forces Reduced Memory Usage for Unusual Simulations Memory usage for simulations of large highly bonded structures such as covalent crystals and for sparse simulations such as coarse grained models has been greatly reduced without affecting the performance of typical biopolymer simulations Support for CHARMM 31 Stream Files and CMAP Crossterms Both NAMD and psfgen standalone or VMD plug read and interpret the new CHARMM 31 stream files combining topology and parameters and the new CMAP crossterm dihedral dihedral potential function Support for OPLS Force Field Geometric combining of Lennard Jones radius parameters oij 0 05 as required by the OPLS force field is available with the option vdwGeometricSigma 1 2 NAMD and molecular dynamics simulations Molecular dynamics MD simulations compute atomic trajectories by solving equations of motion numerically using empi
97. eps 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 output of NAMD If specified and nonzero atomic and group pressure tensors will be output to stdout e outputTiming lt timesteps between timing output gt Acceptable Values nonnegative integer Default Value the greater of firstLdbStep or 10x outputEnergies 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 AM
98. f 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 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 o
99. fects in constant energy simulations are much easier to spot in TOTAL3 than in TOTAL or TOTAL2 PRESSURE is the pressure calculated based on individual atoms while GPRESSURE incor porates hydrogen atoms into the heavier atoms to which they are bonded producing smaller fluc tuations The TEMPAVG PRESSAVG and GPRESSAVG are the average of temperature and pressure values since the previous ENERGY output for the first step in the simulation they will be identical to TEMP PRESSURE and GPRESSURE e outputEnergies lt timesteps between energy output gt 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 timest
100. ficial 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 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 TT 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 t
101. 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 6 7 Free Energy of Conformational Change Calculations NAMD incorporates methods for performing free energy of conformational change perturbation calculations The system is efficient if only a few coordinates either of individual atoms or centers 82 of mass of groups of atoms are needed The following configuration parameters are used to enable free energy perturbation e freeEnergy lt is free energy perturbation active gt Acceptable Values on or off Default Value off Description Specifies whether or not free energy perturbation is active If it is set to off then no free energy perturbation is performed If it is set to on then the free energy perturbation calculation specified in freeEnergyConfig parameters is executed e freeEnergyConfig lt free energy perturbation script gt Acceptable Values file or script Description Must contain either the name of a free energy perturbation 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 app
102. g 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 5 3 3 Basic dynamics e 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 are excluded and all pairs that match the 1 4 criteria are modified The electrostatic interactions for such pairs are modified by the constant factor defined by 1 4scaling The van der Waals interactions are modified by using the special 1 4 parameters defined in the parameter files e temperature lt in
103. h psfgen command 37 pdb psfgen command 36 pdbalias atom psfgen command 39 pdbalias residue psfgen command 35 PME parameter 52 PMEGridSizeX parameter 52 PMEGridSizeY parameter 52 PMEGridSizeZ parameter 52 PMEGridSpacing parameter 52 PMEInterpOrder parameter 52 PMEProcessors parameter 52 PMETolerance parameter 52 PRESSAVG 23 pressureProfile parameter 108 pressureProfileAtomTypes parameter 109 pressureProfileAtomTypesCol parameter 109 pressureProfileAtomTypesFile parameter 109 pressureProfileEwald parameter 109 pressureProfileEwaldX parameter 109 pressureProfileEwaldY parameter 109 pressureProfileEwaldZ parameter 109 pressureProfileFreq parameter 108 pressureProfileSlabs parameter 108 print command 16 psfcontext create psfgen command 38 psfcontext delete psfgen command 38 psfcontext eval psfgen command 38 psfcontext psfgen command 38 psfcontext reset psfgen command 38 131 psfcontext stats psfgen command 38 readexclusions parameter 24 readpsf psfgen command 39 reassignFreq parameter 61 reassignHold parameter 61 reassignIncr parameter 61 reassignTemp parameter 61 regenerate psfgen command 37 reinitvels command 17 reloadCharges command 17 replica exchange 110 rescaleFreq parameter 60 rescaleTemp parameter 61 rescalevels command 17 resetpsf psfgen command 38 residue psfgen command 36 restartfreq parameter 22 restartname parameter 21 restartsave parameter 22 restraintList pa
104. he ensemble average of equation 9 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 It may be used in conjunction with a soft core potential see relevant section 6 9 4 Description of FEP simulation output The fepOutFile contains electrostatic and van der Waals energy data calculated for lambda and lambda written every fepOutFreq steps The column dE is the energy difference of the single con figuration 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 simulation The cumulative average energy dE_avg value may be summed using the trapezoidal rule to obtain an approximate thermodynamic integration TI estimate for the free energy change during the run Whereas the FEP module of NAMD supplies free energy differences determined from eq
105. he three intra partition interactions will be reported in the following order 1 1 1 2 1 3 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 e pressureProfileAtomTypesFile lt Atom type partition assignments gt Acceptable Values PDB file Default Value coordinate file Description If pressureProfileAtomTypes is greater than 1 NAMD will assign atoms to types based on the corresponding value in pressureProfileAtomTypesCol The type for each atom must be strictly less than pressureProfileAtomTypes e pressureProfileAtomTypesCol lt pressureProfileAtomTypesFile PDB column gt Acceptable Values PDB file 109 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
106. he switching function should start taking effect to bring the van der Waals potential to 0 smoothly at the cutoff distance Thus the value of switchdist must always be less than that of cutoff 5 1 2 Non bonded 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 Al 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 energy N 0 cutoff distance Figure 2 Graph showing an electrostatic potential with and without the application of the shifting function Next consider the case where full electrostatics are calculated In this case the electrostatic interactions are not truncated at any distance In this s
107. ibute 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 PERFORMANCE 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
108. ification of the keywords is case insensitive so that any combination of upper and lower case letters will have the same meaning Hence DCDfile and dcdfile are equivalent The capitalization in the values however may be important Some values indicate file names in which capitalization is critical Other values such as on or off are case insensitive 2 2 2 Tcl scripting interface and features When compiled with Tcl all released binaries the config file is parsed by Tcl in a fully backwards compatible manner with the added bonus that any Tcl command may also be used This alone allows e the source command to include other files works w o 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
109. ihedrals Purpose Remove all angles and or dihedrals and completely regenerate them using the segment automatic generation algorithms This is only needed if patches were applied that do not correct angles and bonds Segment and file defaults are ignored and angles dihedrals for the entire molecule are regenerated from scratch Arguments angles Enable generation of angles from bonds dihedrals Enable generation of dihedrals from angles Context After one or more segments have been built 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 onl
110. ile the coodinates that frames are fit to by show replicas vmd e g a folded structure e server port the port to connect to the replica server on and 111 e 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 set set set set set set set set set set set set set set set e alanin base namd basic config options for NAMD e alanin params parameters e alanin psf structure e unfolded pdb initial coordinates e alanin pdb folded structure for fitting in show_replicas vmd e fold_alanin conf config file for replica_exchange tcl script e restart_1 conf config file to continue alanin folding another 10 ns and e load_all vmd load all output into VMD and color by target temperature The fold_alanin conf config file contains the following settings 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 list beirut belfast 112 7 Translation bet
111. iles NAMD generates a xsc eXtended System Configuration file which contains the periodic cell parameters and extended system variables such as the strain rate in constant pressure simulations Periodic cell parameters will be read from this file if this option is present ignoring the above parameters e XSTfile lt XST file to write cell trajectory to gt Acceptable Values file name 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 64 e 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 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
112. imesteps i e the r RESPA integrator is used For appropriate values of k it is believed that the error introduced by this infrequent evaluation is modest compared to the error already incurred by the use of the numerical Verlet integrator Improved methods for incorporating these long range forces are currently being investigated with the intention of improving accuracy as well as reducing the frequency of long range force evaluations In the scheme described above the van der Waals forces are still truncated at the local interac tion distance Thus the van der Waals cutoff distance forms a lower limit to the local interaction distance While this is believed to be sufficient there are investigations underway to remove this limitation and provide full van der Waals calculations in O N time as well 5 3 NAMD configuration parameters 5 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 Default Value 1 0 Description The timestep size to use when integrating each step of the simulation The value is specified in femtoseconds e firsttimestep lt starting timestep value gt Acceptable Values non negative integer Default Value 0 Descriptio
113. inates 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 langevinCol lt column of PDB from which to read coefficients gt Acceptable Values X Y Z 0 or B 59 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 6 3 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 7 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
114. ing 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 e pressureProfileEwaldX lt Ewald grid size along X gt Acceptable Values Positive integer Default Value 10 Description e pressureProfileEwaldY lt Ewald grid size along Y gt Acceptable Values Positive integer Default Value 10 Description e pressureProfileEwaldZ lt Ewald grid size along Z gt Acceptable Values Positive integer Default Value 10 Description e 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 t
115. ing parameter A specified in a conformational forcing calculation For example the restraint distance dref depends on A and as A changes two atoms or centers of mass are forced closer together or further apart In this case Ky Kyo the value supplied at input Alternatively the value of Kf may depend upon the coupling parameter according to Ky KjoA Bounds Position bound 1 atom Force constant K reference position Fref and upper or lower reference distance dref Upper bound E Ky 2 di dref for di gt dref else E 0 Lower bound E K5 2 di dre for di lt dref else E 0 di P Trefl Distance bound 2 atoms Force constant Kf and upper or lower reference distance dref Upper bound E K5 2 dij dref for dij gt dref else E 0 Lower bound E K5 2 dij dref for dij lt dref else E 0 Angle bound 3 atoms Force constant Ky and upper or lower reference angle Oref Upper bound E Ky 2 0 bref for 0 gt Ores else E 0 Lower bound E K5 2 0 bref for O lt Ores else E 0 Torsion bound 4 atoms An upper and lower bound must be provided together Energy gap Eo lower AND upper reference angles x and xa and angle interval Ax a aX lt xX2 E 0 Ga AX lt x lt x E G 2 1 cos x x1 X2 lt x x2 4x E G 2 1 cos x x2 x2 4Ax lt x x 4x 27 E G G Eo 1 cos Ax Bounds may be use
116. ique des assemblages membranaires UMR CNRS UHP 7565 Universit Henri Poincar BP 239 54506 Vandeeuvre ls Nancy cedex France 2001 2006 CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE 6 9 1 Introduction Theoretical background A method to perform alchemical free energy perturbation FEP 32 4 31 29 19 14 21 9 10 is available in NAMD Within the FEP framework the free energy difference between two alternate states a and b is expressed by NE 7 In exp 6 Hi x pa Hala Px q 8 Here 67 kgT where kg is the Boltzmann constant T is the temperature Ha X Px and Hp x Px are the Hamiltonians characteristic of states a and b respectively denotes an ensemble average over configurations representative of the initial reference state a Convergence of equation 8 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 corre sponding ensembles see Figure 5 In practice 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 a general extent parameter often referred to as coupling parameter 4 21 17 18 A that makes the Hamiltonian and hence the free energy a continuous function of this parameter between a and b
117. itial 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 48 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 zeroMomentum lt remove center of mass drift due to PME gt Acceptable Values yes or no Default Value no Description If enabled the net momentum of the simulation and any resultant drift is removed before every full electrostatics step This correction should conserve energy and have minimal impact on parallel scaling This feature should only be used for simulations that would conserve momentum except for the slight errors in PME Features such as fixed atoms harmonic restraints steering forces and L
118. its instantaneous component Fg only the average force F is physically meaningful In the framework of the average biasing force ABF approach 11 24 F is accumulated in small windows or bins of finite size thereby providing an estimate of the derivative dA amp d amp defined in equation 6 The force applied along the reaction coordinate to overcome free energy barriers is defined by 6 FAPF Vy A Feje Ve 7 where A denotes the current estimate of the free energy and Fe e the current average of Fe As sampling of the phase space proceeds the estimate Vp Ais progressively refined The biasing force F introduced in the equations of motion guarantees that in the bin centered about the force acting along the reaction coordinate averages to zero over time Evolution of the system along is therefore governed mainly by its self diffusion properties A particular feature of the instantaneous force F is its tendency to fluctuate significantly As a result in the beginning of an ABF simulation the accumulated average in each bin will generally take large inaccurate values Under these circumstances applying the biasing force along according to equation 7 may severely perturb the dynamics of the system thereby biasing artificially the accrued average and thus impede convergence To avoid such undesirable effects no biasing force is applied in a bin centered about until a r
119. l 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 Description Angular velocity of rotation degrees timestep 6 6 5 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 current coordinates The force on each atom is given by the gradient of the potential Urmp ae RM S t RMS t 2 where RMS t is the instantaneous best fit RMS distance of the current coordinates from the target coordinates and RMS 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
120. l 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 stiffmess 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 kcal mol A in the 71 pdb file the force actually calculated is F 2K 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 wil
121. lRMSD with the same value in each NAMD input file and use the NAMD parameter firstTimestep in the continuation runs so that the target RMSD continues from where the last run left off TMDFinalRMSD lt target RMSD at last TMD step gt Acceptable Values Non negative value in A Default Value 0 Description If no TMDInitialRMSD is given the initial RMSD will be calculated at the first TMD step TMDFinalRMSD may be less than or greater than TMDInitialRMSD depending on whether the system is to be steered 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 6 6 6 Steered Molecular Dynamics SMD The SMD feature is independent from the harmonic constraints although it follows the same ideas In both SMD and harmonic constraints one specifies a PDB file which indicates which atoms are tagged as constrained The PDB file also gives initial coordinates for 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 73 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
122. le Values args Description The string or Tcl list provided by this option is appended to the tcIBC calcforces command arguments This parameter may appear multiple times during a run in order to alter the parameters of the boundary potential function The script provided in tclBCScript and the calcforces procedure it defines are executed in multiple Tcl interpreters one for every processor that owns patches These tcl1BC interpreters do not share state with the Tcl interpreter used for tclForces or config file parsing The calcforces procedure is passed as arguments the current timestep a unique flag which is non zero for exactly one Tcl interpreter in the simulation that on the processor of patch zero and any arguments 79 provided to the most recent tclBCArgs option The unique flag is useful to limit printing of messages since the command is invoked on multiple processors The print vecadd vecsub vecscale getbond getangle getdihedral anglegrad and dihedralgrad commands described under tclForces are available at all times The wrapmode lt mode gt command available in the tclBCScript or the calcforces procedure determines how coordinates obtained in the calcforces procedure are wrapped around periodic boundaries The options are e patch default the position in NAMD s internal patch data structure requires no extra calculation and is almost the same as cell e input the position corresponding to the inp
123. led description of this feature see next subsection applyBias lt Apply a biasing force in the simulation gt Acceptable Values yes or no Default Value yes Description By default a biasing force is applied along the reaction coordinate in ABF calculations It may be however desirable to set this option to no to monitor the evolution of the system along and collect the forces and the free energy yet without introducing any bias in the simulation usMode lt Run umbrella sampling simulation gt Acceptable Values yes or no 97 Default Value no Description When setting this option an umbrella sampling 30 calculation is per formed supplying a probability distribution for the reaction coordinate As an initial guess of the biases required to overcome the free energy barriers use can be made of a pre vious ABF simulation cf inFiles In addition specific restraints may be defined using the restraintList feature described below 6 8 4 Including restraints in ABF simulations In close connection with the possibility to run umbrella sampling simulations the ABF module of NAMD also includes the capability to add sets of restraints to confine the system in selected regions of configurational space Incorporation of harmonic restraints may be invoked using a syntax similar in spirit to that adopted in the conformational free energy module of NAMD abf restraintList anglel angle A 1 CA G 1 N3
124. ll push atoms toward the center and a negative value will pull atoms away from the center e cylindricalBCexp2 lt exponent for second potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for second boundary potential The only likely values to use are 2 and 4 6 4 3 Periodic boundary conditions NAMD provides periodic boundary conditions in 1 2 or 3 dimensions The following parameters are used to define these boundary conditions e cellBasisVectori lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellBasisVector2 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellBasisVector3 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellOrigin lt center of periodic cell A gt Acceptable Values position Default Value 000 Description When position rescaling is used to control pressure this location will remain constant Also used as the center of the cell for wrapped output coordinates e extendedSystem lt XSC file to read cell parameters from gt Acceptable Values file name Description In addition to coor and vel output f
125. lso be used for PDB format coordinate file When gromacs is set to on either grocoorfile or coordinates must be defined but not both However NAMD does not have support for many GROMACS specific options e Dummies fake atoms with positions generated from the positions of real atoms are not supported e The GROMACS pairs section where explicit 1 4 parameters are given between pairs of atoms is not supported since NAMD calculates its 1 4 interactions exclusively by type e Similarly exclusions are not supported The biggest problem here is that 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 re
126. lue none Description Output file containing a distribution of the instantaneous components of the force Fg for every bin comprised between xiMin and xiMax This is useful for performing error analysis for the resulting free energy profile fMax lt Half width of the force histograms gt Acceptable Values positive decimal number in kcal mol A Default Value 60 0 Description When force distributions are written in distFile the histogram collects Fg values ranging from fMax to fMax moveBoundary lt Number of samples beyond which xiMin and xiMax are updated gt Acceptable Values positive integer Default Value 0 Description Slow relaxation in the degrees of freedom orthogonal to the reaction coordi nate results in a non uniform sampling along the latter To force exploration of in quasi non ergodic situations the boundaries of the reaction pathway may be modified dynamically when a preset minimum number of samples is attained As a result the interval between xiMin and xiMax is progressively narrowed down as this threshold is being reached for all values of It should be clearly understood that uniformity of the sampling is artificial and is only used to force diffusion along Here uniform sampling does not guarantee the proper convergence of the simulation restraintList lt Apply external restraints gt Acceptable Values list of formatted entries Default Value empty list Description For a detai
127. lues positive integer Default Value 1 Description The frequency in timesteps with which the current SMD data values are printed out 6 6 7 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 Description This is a free port number on the machine that node 0 is running on This number will have to be entered into VMD e IMDfreq lt timesteps between sending coordinates gt Acceptable Values positive integer Description This allows coordinates to be sent less often which may increase NAMD performance or be necessary due to a slow network e IMDwait lt wait for an IMD connection gt Acceptable Values yes or no Default Value no Description If no NAMD will proceed with calculations whether a connection is present or not If yes NAMD will pause at startup until a connection is made and pause when the connection is lost e IMDignore lt ignore interactive steering forces gt Acceptable Values yes or no Default Value no Description If yes NAMD will ign
128. mbles of particles from an infinite separation to some contact distance 8 w 1 3 Inglr 4 p Here g r is the pair correlation function of the two particles or ensembles thereof The vocabulary PMF has however been extended to a wide range of reaction coordinates that go far beyond simple interatomic or intermolecular distances In this perspective generalization of equation 4 is not straightforward This explains why it may be desirable to turn to a definition suitable for any type of reaction coordinate 1 A ge ra 5 A is the free energy of the state defined by a particular value of which corresponds to an iso hypersurface in phase space Ay is a constant and P is the probability density to find the chemical system of interest at 92 The connection between the derivative of the free energy with respect to the reaction coordinate dA d and the forces exerted along the latter may be written as 28 12 dA 0V 10M JN de ae BOE i Fede where J is the determinant of the Jacobian for the transformation from generalized to Cartesian coordinates The first term of the ensemble average corresponds to the Cartesian forces exerted on the system derived from the potential energy function V x The second contribution is a geometric correction arising from the change in the metric of the phase space due to the use of generalized coordinates It is worth noting that contrary to
129. n 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 e 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 1 5 3 2 Simulation space partitioning 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 1 for more information 45 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 1 If switching is set to on then switchdist must also be defined e switchdist 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
130. n 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 6 5 1 Berendsen pressure bath coupling NAMD provides constant pressure simulation using Berendsen s method The following parameters are used to define the algorithm e BerendsenPressure lt use Berendsen pressure bath coupling gt Acceptable Values on or off 66 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 la
131. n between NAMD and X PLOR configuration parameters 113 8 Sample configuration files 115 9 Running NAMD 120 9 1 Mac OS X Users Must Install the IBM XL C C Run Time Library 120 9 2 Individual Windows Linux Mac OS X or Other Unix Workstations 120 9 3 Linux Mac OS X or Other Unix Workstation Networks 121 9 4 Windows Workstation Networks 0 0 0 00 0b eee ee ee eee 122 9 5 BProc Based Clusters Scyld and Clustermatic o o e 122 905 GS GATX aa a e A A a tcp ahh O A 123 9 7 Compaq AlphaServer SC 123 9 8 IBM POWER Clusters 0 0 ee ee 123 9 9 Origin 20007 parann ek ab a BOM A ee ee A OR a 123 9 10 Memory Usage cari gee oye cps a a Dip Sod Pee e 124 9 11 Improving Parallel Scaling e 124 10 NAMD Availability and Installation 126 10 1 How to obtain NAMD 2 ee 126 10 2 Platforms on which NAMD will currently TUNA o o e 126 10 3 Complline NAMD ra eu ats eee a A A eg 126 10 4 Documentation 220405 2 S38 in hk AA Boe go oe e BR AS 126 References 127 Index 129 List of Figures OH WN rH 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 Convergence of an FEP calculation If the ensembles rep
132. n have values only in the range from 0 to 1 and a value of A 0 corresponds to one defined state and a value of A 1 corresponds to the other defined state Intermediate values of correspond to intermediate states in the case of conformational forcing calculations these intermediate states are physically realizable but in the case of molecular transformation calculations they are not The value of A is changed during the simulation In the first method provided here the change in A is stepwise while in the second method it is virtually continuous Multi configurational thermodynamic integration MCTI In MCTI one accumulates OU OA at several values of A and from these averages estimates the integral AA f OU OA dr With this method the precision of each 9U 0A can be estimated from the fluctuations of the time series of JU 0A Slow growth In slow growth A is incremented by A 1 Nstep after each dynamics integration time step and the pmf is estimated as AA Y OU OX A Typically slow growth is done in cycles of equilibration at A 0 change to A 1 equilibration at A 1 change to A 0 It is usual to estimate the precision of slow growth simulations from the results of successive cycles 6 7 3 Options for Conformational Restraints User supplied restraint and bounds specifications urestraint n restraint or bound specification see below Restraint Specifications not coupled to pmf calculations
133. n 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 module has been designed to make it easy for users to add additional measure commands e The coorfile command allows NAMD to perform force and energy analysis on trajectory files coorfile open dcd filename opens the specified DCD file for reading coorfile read reads the next frame in the opened DCD file replacing 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 6 11 for details as well as the example scripts in Sec 8 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
134. nerating PSF and PDB files for use with NAMD will typically consist of the following steps 1 Preparing separate PDB files containing individual segments of protein solvent etc before running psfgen 2 Reading in the appropriate topology definition files and aliasing residue and atom names found in the PDB file to those found in the topology files This will generally include selecting a default protonation state for histidine residues 3 Generating the default structure using segment and pdb commands 4 Applying additional patches to the structure 5 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
135. ng wisdom generated by performance measurements to the same file for future use This will reduce startup time when running the same size PME grid on the same number of processors as a previous run using the same file 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 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 this 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 3 6 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
136. ns s seii a a See eee he aes GRAPE 61 6 4 1 Spherical harmonic boundary conditions 2 61 6 4 2 Cylindrical harmonic boundary conditions 62 6 4 3 Periodic boundary conditions 02 0000 eee eee 64 6 5 t Pressure Control sen eh a ae eat a BAK eae a a ee ie eee 65 6 5 1 Berendsen pressure bath coupling 0 2 e e 66 6 5 2 Nos Hoover Langevin piston pressure control 2 4 67 6 6 Applied Forces and Analysis 2 a 69 6 6 1 Constant Forces ee ee 69 6 6 2 External Electric Field 2 2 0 0 0 0202000022 eee eee 70 6 6 3 Moving Constraints 2 2 0 0000 ee ee 70 6 6 4 Rotating Constraints s osoo e e e 71 6 6 5 Targeted Molecular Dynamics TMD 72 6 6 6 Steered Molecular Dynamics SMD o 73 6 6 7 Interactive Molecular Dynamics IMD 75 6 6 8 Tcl Forces and Analysis a 75 6 6 9 Tcl Boundary Forces ssc ec ese Gok be pe a ee eee RO 79 6 6 10 External Program Forces 2 0 0 02 eee ee 82 6 7 Free Energy of Conformational Change Calculations 82 6 7 1 User Supplied Conformational Restraints 0 00004 83 6 7 2 Free Energy Calculations sooo a 84 6 7 3 Options for Conformational Restraints 0 0 000 000 08 85 6 7 4 Options for ATOM Specification 0 e 86 6 7 5 Options for Potential of Mean Force Calcula
137. nstrained 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 rigidIterations lt maximum ShakeH iterations gt Acceptable Values positive integer Default Value 100 Description The maximum number of iterations ShakeH will perform before giving up on constraining the bond lengths If the bond lengths do not converge a warning message is printed and the atoms are left at the final value achieved by ShakeH Although the default value is 100 convergence is usually reached after fewer than 10 iterations rigidDieOnError lt maximum ShakeH iterations gt Acceptable Values on or off Default Value on Description Exit and report an error if rigidTolerance is not achieved after rigidItera tions 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 4 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 ma
138. 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 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 used 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 51 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 5 PME parameters PME stands for Particle Mesh Ewald
139. obtained directly from the parameter file and the full multiplicity will be used same behavior as in CHARMM If the PSF file originates from X PLOR consecutive multiple entries for the same dihedral indicating the dihedral multiplicity for X PLOR will be ignored e velocities lt velocity PDB file gt Acceptable Values UNIX filename Description The PDB file containing the initial velocities for all atoms in the simulation This is typically a restart file or final velocity file written 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 th
140. of forces e tCoupleFile lt PDB file with tCouple parameters gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to use for the temperature coupling coefficient for each atom If this parameter is not specified then the PDB file specified by coordinates is used e tCoupleCol lt column of PDB from which to read 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 3 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 60 e rescaleTemp lt temperature for equilibration K gt Acceptable Values positive decimal Descrip
141. of the simulation 7 e A4 1 For intermediate values of A both the alanine and the glycine side chains participate in non bonded 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 Construction of an appropriate list of excluded atoms common to the two alternate topologies is therefore necessary 101 Hi oe i a H F Na NS e o Ce H KA E Figure 6 Dual topology description for an alchemical simulation Case example of the mutation of alanine into serine The lighter color denotes the non interacting alternate state It is also worth noting that the free energy calculation does not alter intramolecular potentials e g bond stretch valence angle deformation and torsions in the course of the simulation In cal culations 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 thermo dynamic cycle perturbation of intramolecular terms may by and large be safely avoided 5 6 9 2 Implementation of free energy perturbation in NAMD The procedure implemented in NAMD is particularly adapted for performing free energy calcula tions that split the A reaction path into a number of
142. on 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 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 e splitPatch lt how to assign atoms to patches gt Acceptable Values position or hydrogen Default Value hydrogen 46 Description When set to hydrogen hydrogen atoms are kept on the same patch as their parents allowing faster distance checking and rigid bonds hgroupCutoff A lt used for group based distance testing gt Acceptable Values positive decimal Default Value 2 5 Description This should be set to twice the largest distance which will ever occur between a hydrogen atom and its mother Warnings will be printed if this is not the case This value is also added to the margin margin lt extra length in patch dimension A gt Accep
143. orce evaluation taking all atom coordinates as input e 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 e extForcesCommand lt Force calculation command gt Acceptable Values UNIX shell command Description This string is the argument to the system function at every forces evaluation and should read coordinates from the file specified by extCoordFilename and write forces to the file specified by extForceFilename e extCoordFilename lt Temporary coordinate file gt Acceptable Values UNIX filename Description Atom coordinates are written to this file which should be read by the extForcesCommand The format is one line of atomid charge x y z for every atom followed by three lines with the periodic cell basis vectors a x a y a z b x b y b z and c x c y c z The atomid starts at 1 not 0 For best performance the file should be in tmp and not on a network mounted filesystem e extForceFilename lt Temporary force file gt Acceptable Values UNIX filename Description Atom forces are read from this file after extForcesCommand in run The format is one line of atomid replace fx fy fz for every atom followed by the energy on a line by itself and then optionally three lines of the virial v xx v xy v xz v yx v yy v yz V ZX v zy v zz where e g v xy fx y
144. ordpdb May call multiple times coord lt segid gt lt resid gt lt atomname gt lt z y z gt Purpose Set coordinates for a single atom Arguments lt segid gt Segment ID of target atom lt resid gt Residue ID of target atom lt atomname gt Name of target atom lt x y z gt Coordinates to be assigned Context After structure has been generated coordpdb lt file name gt segid 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
145. ore any steering forces generated by VMD to allow a simulation to be monitored without the possibility of perturbing it 6 6 8 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 79 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 6 6 9 The following configuration parameters are used to enable the Tcl interface e tclForces lt is Tcl interface active gt Acceptable Values on or off Default Value off Description Specifies whether or not Tcl interface is active If it is set to off then no Tcl code is executed If it is set to on then Tcl code specified in tclForcesScript parameters is executed e tclForcesScript lt input for Tcl interface gt Acceptable Values file or script Description Must contain either the name of a Tcl script file or the script itself between and may include multiple lines This parameter may occur multiple times and scripts will be executed in order of appearance The script s should perform any required initialization on the Tcl interpreter including requesting data needed during the first timestep and define a procedure calcforces to be called every
146. primary structure of the segment including auto first last residue pdb etc Context After topology definitions and residue aliases May call multiple times Structure information is generated at the end of every segment command auto angles dihedrals none Purpose Override default settings from topology file for automatic generation of angles and dihedrals for the current segment Arguments angles Enable generation of angles from bonds dihedrals Enable generation of dihedrals from angles none Disable generation of angles and dihedrals Context Anywhere within segment does not affect later segments first lt patch name gt Purpose Override default patch applied to first residue in segment Default is read from topology file and may be residue specific Arguments lt patch name gt Single target patch residue name or none Context Anywhere within segment does not affect later segments last lt patch name gt Purpose Override default patch applied to last residue in segment Default is read from topology file and may be residue specific Arguments lt patch name gt Single target patch residue name or none Context Anywhere within segment does not affect later segments residue lt resid gt lt resname gt chain Purpose Add a single residue to the end of the current segment Arguments lt resid gt Unique name for residue 1 5 characters usually numeric lt resname gt Residue type name from
147. 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 124 Charm The new NPTL pthreads library in RedHat 9 fixes these problems so an SMP port can become the standard shipping binary version in the future On some large machines with very high bandwidth interconnects you may be able to in crease performance for PME simulations by adding either strategy USE_MESH or strategy USE_GRID to the command line These flags instruct the Charm communication optimization library to reduce the number of messages sent during PME 3D FFT by combining data into larger messages to be transmitted along each dimension of either a 2D mesh or a 3D grid respectively While reducing the number of messages sent per processor from N to 2 sqrt N or 3 cbrt N the total amount of data transmitted for the FFT is doubled or tripled 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 NA
148. ption 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 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 De
149. r ensemble averaging Yet it is recommended to update fepOutFile energies at longer intervals to avoid large files containing highly correlated data e fepOutFile lt FEP energy output filename gt Acceptable Values filename Default Value outfilename Description An output file named fepOutFile generated by NAMD contains the FEP energies dumped every fepOutFreq steps 6 9 3 Examples of input files for running FEP alchemical 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 1 103 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 ion fepout Output file containing the free energy fepUutFreq 5 Frequency at which fepOutFreq is updated fepEquilSteps 5000 Number of equilibration steps per A state set step 0 0 Starting value of A set dstep 0 1 Increment of A e 04 while step lt 1 0 4 TCL script to increment A lambda step 1 set lambda value set step expr step dstep 2 increment A lambda2 step 3 set lambda2 value f run 10000 4 run 10 000 MD steps The user should be reminded that by setting run 10000 10 000 MD steps will be performed which includes the preliminary fepEquilSteps equilibration steps This means that here t
150. rameter 103 FFTWEstimate parameter 53 FFTWUseWisdom parameter 53 FFTWWisdomFile parameter 53 first psfgen command 36 firsttimestep parameter 45 fixedAtoms parameter 57 fixedAtomsCol parameter 58 fixedAtomsFile parameter 57 fixedAtomsForces parameter 57 MA parameter 51 MAFFT parameter 51 MAFFTBlock parameter 51 MALevels parameter 51 MAMp parameter 51 MAtheta parameter 51 fMax parameter 97 forceConst parameter 95 freeEnergy parameter 83 freeEnergyConfig parameter 83 FullDirect parameter 53 fullElectFrequency parameter 54 fullSamples parameter 96 F F F F F F GPRESSAVG 23 GPRESSURE 23 grocoorfile parameter 27 gromacs parameter 26 grotopfile parameter 27 guesscoord psfgen command 39 hgroupCutoff A parameter 47 historyFile parameter 96 IMDfreq parameter 75 IMDignore parameter 75 IMDon parameter 75 IMDport parameter 75 IMDwait parameter 75 inFiles parameter 96 lambda parameter 102 lambda2 parameter 102 langevin parameter 59 langevinCol parameter 59 langevinDamping parameter 59 langevinFile parameter 59 langevinHydrogen parameter 59 LangevinPiston parameter 68 LangevinPistonDecay parameter 68 130 LangevinPistonPeriod parameter 68 LangevinPistonTarget parameter 68 LangevinPistonTemp parameter 68 langevinTemp parameter 59 last psfgen command 36 les parameter 105 lesCol parameter 106 lesFactor parameter 106 lesFile parameter 106 lesReduce
151. rameter 97 rigidBonds parameter 50 rigidDieOnError parameter 50 rigidIterations parameter 50 rigidTolerance parameter 50 rotConsAxis parameter 72 rotConsPivot parameter 72 rotConstraints parameter 72 rotConsVel parameter 72 run command 16 scnb parameter 24 seed parameter 49 segment psfgen command 35 selectConstraints parameter 57 selectConstrX parameter 57 selectConstrY parameter 57 selectConstrZ parameter 57 MD parameter 74 MDDir parameter 75 MDFile parameter 74 MDk parameter 74 MDOutputFreq parameter 75 MDVel parameter 74 source command 16 sphericalBC parameter 62 sphericalBCCenter parameter 62 S S S S S S sphericalBCexp1 parameter 62 sphericalBCexp2 parameter 62 sphericalBCk1 parameter 62 sphericalBCk2 parameter 62 sphericalBCr1 parameter 62 sphericalBCr2 parameter 62 splitPatch parameter 46 stepspercycle parameter 45 StrainRate parameter 69 structure parameter 20 Surface TensionTarget parameter 69 switchdist parameter 46 switching parameter 46 tclBC parameter 79 tclBCArgs parameter 79 tclBCScript parameter 79 tclForces parameter 76 tclForcesScript parameter 76 tCouple parameter 60 tCoupleCol parameter 60 tCoupleFile parameter 60 tCoupleTemp parameter 60 TEMPAVG 23 temperature parameter 48 timestep parameter 45 MD parameter 72 MDFile parameter 73 MDFinalRMSD parameter 73 MDFirstStep parameter 73 MDInitialRMSD parameter 73 MDk parameter
152. rameter NBXMod Both parameters specify which atom pairs to exclude from non bonded interactions The ability to ignore explicit exclusions is not present within NAMD thus only positive values of NBXMod have NAMD equivalents These equivalences are NBXMod 1 is equivalent to exclude none no atom pairs excluded NBXMod 2 is equivalent to exclude 1 2 only 1 2 pairs excluded NBXMod 3 is equivalent to exclude 1 3 1 2 and 1 3 pairs excluded NBXMod 4 is equivalent to exclude 1 4 1 2 1 3 and 1 4 pairs excluded NBXMod 5 is equivalent to exclude scaled1 4 1 2 and 1 3 pairs excluded 1 4 pairs modified 113 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 T
153. rce 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 6 6 9 Tcl Boundary Forces While the tclForces interface described above is very flexible it is only efficient for applying forces to a small number of pre selected atoms Applying forces individually to a potentially large number of atoms such as applying boundary conditions is much more efficient with the tc1BC facility described below e tclBC lt are Tcl boundary forces active gt Acceptable Values on or off Default Value off Description Specifies whether or not Tcl interface is active If it is set to off then no Tcl code is executed If it is set to on then Tcl code specified in the tc1BCScript parameter is executed e tclBCScript lt input for Tcl interface gt Acceptable Values script Description Must contain the script itself between and may include multiple lines This parameter may occur only once The script s should perform any required initialization on the Tcl interpreter and define a procedure calcforces lt step gt lt unique gt args to be called every timestep e tclBCArgs lt extra args for tclBC calcforces command gt Acceptab
154. re 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 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 47 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 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 monitorin
155. resentative of states a and b are too disparate equation 8 will not converge a If in sharp contrast the configurations of state b form a subset of the ensemble of configurations characteristic of state a the simulation is expected to converge b The difficulties reflected in case a may be alleviated by the introduction of mutually overlapping intermediate states that connect a to b c It should be mentioned that in practice the kinetic contribution 7 p is assumed to be identical for state a and state b 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 STATES ions Sear os A E aoe dd Shae Boar 1 Introduction NAMD is a parallel molecular dynamics program for UNIX platforms designed for high performance simulations in structural biology This document describes how to use NAMD its features and the platforms on which it runs The document is divided into several sections Section 1 gives an overview of NAMD Section 2 lists the basics for getting started Section 3 describes NAMD file formats Section 4 explains PSF file generation with psfgen Section 5 lists basic simulation options Section 6 lists additional simulation options Section 7 provides hints for X PLOR users Section 8 provides sample configuration files Section 9 gives details on running NAMD Section 10 gives details on installing
156. rger 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 not fluctuate randomly during a simulation and the compressibility estimate was exact then the inital pressure would decay exponentially to the target pressure with this time constant Having a longer relaxation time results in more averaging over pressure measure ments and hence smaller fluctuations in the cell volume A reasonable choice for relaxation time would be 100 fs The compressibility and the relaxation time appear only as a ratio in the dynamics so a larger compressibility is equivalent to a smaller relaxation time 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
157. rical 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 22 In order to conduct MD simulations various computer programs have been developed including X PLOR 7 and CHARMM 6 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 11 NAMD was designed to run efficiently on such parallel machines for simulating large molecules NAMD is particularly well suited to the increasingly popular Beowulf class PC clusters which are quite similar to the workstation clusters for which is was originally designed Future versions of NAMD will also make efficient use of clusters of multi processor workstations or PCs NAMD has several important features e Force Field Compatibility The force field used by NAMD is the same as that used by the programs CHARMM 6 and X PLOR 7 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 Electrost
158. rmats include PDB coordinate files and binary DCD trajectory files These similar ities assure that the molecular dynamics trajectories from NAMD can be read by CHARMM or X PLOR and that the user can exploit the many analysis algorithms of the latter packages e Dynamics Simulation Options MD simulations may be carried out using several options including Constant energy dynamics Constant temperature dynamics via Velocity rescaling x Velocity reassignment Langevin dynamics Periodic boundary conditions Constant pressure dynamics via 12 Berendsen pressure coupling 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 it 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
159. rns the charge of the current atom e getid Returns the 1 based ID of the current atom 80 e addforce lt fx gt lt fy gt lt fz gt Adds the specified force to the current atom for this step e addenergy lt energy gt Adds potential energy to the BOUNDARY column of NAMD output As an example these spherical boundary condition forces sphericalBC on sphericalBCcenter 0 0 0 0 0 0 sphericalBCri 48 sphericalBCk1 10 sphericalBCexp1 2 Are replicated in the following script tc1BC on tclBCScript proc veclen2 vi foreach x1 y1 z1 v1 break return expr x1 x1 y1x y1 z1 z1 wrapmode input wrapmode cell wrapmode nearest wrapmode patch the default HH H proc calcforces step unique R K if step 20 0 cleardrops if unique print clearing dropped atom list at step step set R expr 1 R set R2 expr R R set tol 2 0 set cut2 expr R tol R tol while nextatom 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 81 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 6 6 10 External Program Forces This feature allows an external program to be called to calculate forces at every f
160. ror dyld namd2 can t open library opt ibmcmp 1ib 1libibmc A dylib 9 2 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 you can run the namd2 binary directly namd2 lt configfile gt For multiprocessor workstations Windows and Solaris released binaries are based on SMP versions of Charm that can run multiple threads For best performance use one thread per processor with the p option namd2 p lt procs gt lt configfile gt Since the SMP versions of NAMD are relatively new there may be bugs that are only present when running multiple threads You may want to try running with charmrun see below if you experience crashes 120 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 9 3 Linux Mac OS X or Other Unix Workstation Networks The same binaries used for individual workstations as described above 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
161. row time T fs ps or ns default ps lambda Y value of A only needed for stop and nogrow lambdat Z value of A only needed for grow fade and nogrow default 0 print P fs ps or ns or noprint default ps up down stop A is applied to the reference values grow fade nogrow is applied to Ky A fixed value A is used to determine the ref values up grow A changes from 0 1 no value of A is required down fade A changes from 1 gt 0 no value of A is required stop nogrow dU dA is accumulated for single point MCTI Lambda control for automated MCTI meti task stepup stepdown stepgrow or stepfade equiltime T1 fs ps or ns default ps accumtime T2 fs ps or ns default ps numsteps N lambdat Z value of A only needed for stepgrow and stepfade default 0 print P fs ps or ns or noprint default ps stepup stepdown A is applied to the reference values stepgrow stepfade A is applied to Ky A fixed value A is used to determine the ref values stepup stepgrow A changes from 0 1 no value of A is required stepdown stepfade A changes from 1 0 no value of A is required For each task A changes in steps of 1 0 N from 0 1 or 1 gt 0 At each step no data is accumulated for the initial period T1 then dU dA is accumulated for T2 Therefore the total duration of an mcti block is T1 T2 x N 87 6 7 6 Examples Fi
162. s 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 namdOks 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 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
163. s especially the packages X PLOR 7 and CHARMM 6 To achieve this compatibility the set of input files which NAMD uses to define a molecular system are identical to the input files used by X PLOR and CHARMM Thus it is trivial to move an existing simulation from X PLOR or CHARMM to NAMD A description of these molecular system definition files is given in Section 3 1 In addition the output file formats used by NAMD were chosen to be compatible with X PLOR and CHARMM In this way the output from NAMD can be analyzed using X PLOR CHARMM or a variety of the other tools that have been developed for the existing output file 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 NA
164. s 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 new 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 by 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
165. s script Run the psfgen program taking everything until ENDMOL as input You may run psfgen interactively as well Since psfgen is built on a Tcl interpreter you may use loops variables etc but you must use for variables when inside a shell script If you want run psfgen and enter the following commands manually 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
166. s 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 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 Descriptio
167. separate Tcl file Additional RCs tailored for a particular problem may be added by creating a new file providing the required Tcl procedures Existing files such as distance tcl are thoroughly commented and should provide a good basis for the coding of additional coordinates together with 15 1 distance corresponds to the distance separating two selected atoms abf1 index of the first atom of the reaction coordinate abf2 index of the second atom of the reaction coordinate 2 distance com corresponds to the distance separating the center of mass of two sets of atoms e g the distance between the centroid of two benzene molecules abf1 list of indices of atoms participating to the first center of mass abf2 list of indices of atoms participating to the second center of mass 94 3 abscissa corresponds to the distance between the centers of mass of two sets of atoms along a given direction direction a vector Tcl list of three real numbers defining the direction of interest abf1 list of indices of atoms participating to the first center of mass abf2 list of indices of atoms participating to the second center of mass 4 zCoord corresponds to the distance separating two groups of atoms along the z direction of Cartesian space This reaction co ordinate is useful for the estimation of transfer free energies between two distinct media abf1 list of indices of reference atoms abf2 list of indices of atoms of interest
168. ssing hydrogen coordinates are given a default orientation Write structure and coordinate files Now that all of the atoms and bonds have been created we can write out the psf structure file for the system We also create the matching coordinate pdb file The psf and pdb files are a matched set with identical atom ordering as needed by NAMD Using generated files in NAMD The files bpti pdb and bpti psf can now be used with NAMD but the initial coordinates require minimization first The following is an example NAMD configuration file for the BPTI example 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
169. stions are welcome at namd ks uiuc edu We also appreciate hearing about how you are using NAMD in your work 13 1 4 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 The authors would particularly like 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 9 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
170. t 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 e num replicas the number of replica simulations to use e min temp the lowest replica target temperature e max_temp the highest replica target temperature e steps _per_run the number of steps between exchange attempts e num_runs the number of runs before stopping should be divisible by runs_per_frame x frames_per_restart e runs_per_frame the number of runs between trajectory outputs e frames _per_restart the number of frames between restart outputs e namd config file the NAMD config file containing all parameters needed for the simulation except seed langevin langevinDamping langevinTemp outputEnergies outputnane dcdFreq temperature bincoordinates binvelocities or extendedSystem which are provided by replica_exchange tcl e output_root the directory fileroot for output files e psf_file the psf file for show_replicas vmd e initial pdb file the initial coordinate pdb file for show_replicas vmd e fit pdb f
171. t not reciprocal space contributions to the pressure profile Results will be recorded in the NAMD output file in lines with the format PRESSUREPROFILE ts Axx Ayy Azz Bxx Byy Bzz where ts is the timestep followed by the three diagonal components of the pressure tensor in the first slab the slab with lowest z then the next lowest slab and so forth The output will reflect the pressure profile averaged over all the steps since the last output NAMD also reports kinetic bonded and nonbonded contributions separately using the same format as the total pressure but on lines beginning with PPROFILEINTERNAL PPROFILEBONDED and PPROFILENONBONDED pressureProfileSlabs lt Number of slabs in the spatial partition gt Acceptable Values Positive integer Default Value 10 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 108 e 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 script
172. t your local documentation 9 8 IBM POWER Clusters Run the MPI version of NAMD as you would any POE program The options and environment variables for poe are various and arcane so you should consult your local documentation for rec ommended settings As an example to run on Blue Horizon one would specify poe namd2 lt configfile gt nodes lt procs 8 gt tasks_per_node 8 9 9 Origin 2000 For small numbers of processors 1 8 use the non MPI version of namd2 If your stack size limit is unlimited which DQS may do you will need to set it with limit stacksize 64M to run on multiple processors To run on procs processors call the binary directly with the p option namd2 p lt procs gt lt configfile gt For better performance on larger numbers of processors we recommend that you use the MPI version of NAMD To run this version you must have MPI installed Furthermore you must set two environment variables to tell MPI how to allocate certain internal buffers Put the following commands in your cshre or profile file or in your job file if you are running under a queuing system 123 setenv MPI_REQUEST_MAX 10240 setenv MPI_TYPE_MAX 10240 Then run NAMD with the following command mpirun np lt procs gt namd2 lt configfile gt 9 10 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 1
173. table 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 Description Rather than only regenerating the pairlist at the beginning of a cycle regenerate multiple times in order to better balance the costs of atom migration pairlist generation and larger pairlists 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 a
174. table Values positive integer less than numSteps or run Default Value 0 Description In each window fepEquilSteps 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 FEP calculation e fepFile lt pdb file with perturbation flags gt Acceptable Values filename Default Value coordinates Description pdb file to be used for indicating the FEP status for each of the atoms pertaining to the system If this parameter is not declared specifically then the pdb file specified by coordinates is utilized for this information e fepCol lt Column in the fepFile 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 FEP status of each atom 1 e a flag that indicates which atom will be perturbed in the course of the simulation A value of 1 in the specified column indicates the atom will vanish during the FEP calculation whereas a value of 1 indicates that the atom will grow e fepOutFreq lt Frequency of FEP energy output in time steps gt Acceptable Values positive integer Default Value 5 Description Every fepOutFreq number of MD steps the output file fepOutFile is updated by dumping energies that are used for ensemble averaging This variable could be set to 1 to include all the configurations fo
175. tein 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 badwater1 get resid 4 delatom segid resid Have psfgen write out the new psf and pdb file VMD s structure and coordinates are unmodified writepsf myfile_chopwater psf writepdb myfile_chopwater pdb 4 2 BPTI Example To actually run this demo 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 6P
176. tein 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 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 for X ray Crystallography and NMR The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry Yale University 1992 D Chandler Introduction to modern statistical mechanics Oxford University Press 1987 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 E Darve and A Pohorille Calculating free energies using average force J Chem Phys 115 9169 9183 2001 W K den Otter and W J Briels Fre
177. ter file gt Acceptable Values UNIX filename Description A CHARMM19 CHARMM22 or CHARMM27 parameter file that defines all or part of the parameters necessary for the molecular system to be simulated At least one parameter file must be specified for each simulation Multiple definitions but only one file per definition are allowed for systems that require more than one parameter file The files will be read in the order that they appear in the configuration file If duplicate parameters are read a 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
178. 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 is RMS of roughly 100 bar for a 10 000 atom biomolecular system Much larger fluctuations are regularly observed in practice The instantaneous pressure for a biomolecular system is well defined for internal forces that are based on particular periodic images of the interacting atoms conserve momentum and are translationally invariant When dealing with externally applied forces such as harmonic constraints fixed atoms and various steering forces NAMD bases its pressure calculation on the relative 65 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 alter
179. ters 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 105 lesFactor lt number of LES images to use gt Acceptable Values positive integer equal to the number of images present Description This should be equal to the factor used in multiply when creating the structure The interaction potentials for images is divided by lesFactor 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 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 lesReduceMass lt reduce enhanced atom mass gt Acceptable Values on or off Default Value off Description Used with lesReduceTemp to restore velocity dis
180. the BPTI example below If you are using VMD you can also use atom selections to write pieces of the structure to separate files Split a file containing protein and water into separate segments Creates files named myfile_water pdb myfile_frag0 pdb myfile_fragi pdb Requires VMD mol load pdb myfile pdb set water atomselect top water water writepdb myfile_water pdb set protein atomselect top protein set chains lsort unique protein get pfrag foreach chain chains set sel atomselect top pfrag chain sel writepdb myfile_frag chain 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 pro
181. timestep At this point only low level commands are defined In the future this list will be expanded Current commands are e print lt anything gt This command should be used instead of puts to display output For example print Hello World e atomid lt segname gt lt resid gt lt atomname gt Determines atomid of an atom from its segment residue and name For example atomid br 2 N e addatom lt atomid gt Request coordinates of this atom for next force evaluation and the calculated total force on this atom for current force evaluation Request remains in effect until clearconfig is called For example addatom 4 or addatom atomid br 2 N e addgroup lt atomid list gt Request center of mass coordinates of this group for next force evaluation Returns a group ID which is of the form gN where N is a small integer This group ID may then be used to find coordinates and apply forces just like a regular atom ID Aggregate forces may then be applied to the group as whole Request remains in effect until clearconfig is called For example set groupid addgroup 14 10 12 e clearconfig Clears the current list of requested atoms After clearconfig calls to addatom and addgroup can be used to build a new configuration e getstep Returns the current step number 76 e loadcoords lt varname gt Loads requested atom and group coordinates in A into a local array loadcoords should only be called
182. tion 87 6 76 Examples shea a fei lee ae el ee a Pe Oey a BL ae 88 OS Appendix se los dais aie wos ah apache at Gill Gln tele Boe eign Gh eet 90 6 8 Adaptive Biasing Force Calculations 2 2 0 0 00 ee ee 92 6 8 1 Introduction and theoretical background 2 92 6 8 2 Using the NAMD implementation of the adaptive biasing force method 93 6 8 3 Parameters for ABF simulations 2 22200 4 94 6 8 4 Including restraints in ABF simulations o e 98 6 8 5 Important recommendations when running ABF simulations 99 6 8 6 Example of input file for computing potentials of mean force 99 6 9 Alchemical Free Energy Perturbation Calculations 0 100 6 9 1 Introduction 2 6 66 2453 88 ey Sa eG De ee ee eee ee 100 6 9 2 Implementation of free energy perturbation in NAMD 102 6 9 3 Examples of input files for running FEP alchemical calculations 103 6 9 4 Description of FEP simulation output 2 20 4 104 6 10 Locally Enhanced Sampling 2 0 0 00 00 ee ee 105 6 10 1 Structure G n ration ise tir ba bee ee ee eon ee RAO ag 105 610 2 Simulation is A A Gon ue bie haters Go Bark 105 6 11 Pair Interaction Calculations 2 0 0 0 0 002 ee ee ee 106 6 12 Pressure Profile Calculations 0 0 0 0 0 eee ee ee ee 107 6 13 Replica Exchange Simulations 2 0 ee 110 7 Translatio
183. tion Specifies whether or not Langevin piston pressure control is active If set to on then the parameters LangevinPistonTarget LangevinPistonPeriod LangevinPistonDecay and LangevinPistonTemp must be set e LangevinPistonTarget lt target pressure bar gt Acceptable Values positive decimal Description Specifies target pressure for Langevin piston method A typical value would be 1 01325 bar atmospheric pressure at sea level e LangevinPistonPeriod lt oscillation period fs gt Acceptable Values positive decimal Description Specifies barostat oscillation time scale for Langevin piston method If the instantaneous pressure did not fluctuate randomly during a simulation and the decay time was infinite no friction then the cell volume would oscillate with this angular period Having a longer period results in more averaging over pressure measurements and hence slower fluctuations in the cell volume A reasonable choice for the piston period would be 200 fs e LangevinPistonDecay lt damping time scale fs gt Acceptable Values positive decimal Description Specifies barostat damping time scale for Langevin piston method A value larger than the piston period would result in underdamped dynamics decaying ringing in the cell volume while a smaller value approaches exponential decay as in Berendsen s method above A smaller value also corresponds to larger random forces with increased coupling to the Langevin temperature bath T
184. tion Such a setup in which atoms of both the initial and the final states of the system are present in the molecular topology file 1 e the psf file is characteristic of the so called dual topology paradigm 13 23 2 The hybrid Hamiltonian of the system which is a function of the general extent parameter A that connects smoothly state a to state b is calculated as a linear combination of the corresponding Hamiltonians H X Pz A Ho x Px AXHo x px 1 A Hal x Pz 10 where H x pz describes the interaction of the group of atoms representative of the reference state a with the rest of the system H x Px characterizes the interaction of the target topology b with the rest of the system Ho x p is the Hamiltonian describing those atoms that do not undergo any transformation during the MD simulation For instance in the point mutation of an alanine side chain into that of glycine by means of an FEP calculation 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 6 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 0 while the glycine Ca hydrogen atom does not interact with the rest of the protein and vice versa at the end
185. tion The temperature to which all velocities will be rescaled every rescaleFreq timesteps This parameter is valid only if rescaleFreq has been set 6 3 4 Temperature reassignment parameters NAMD allows equilibration of a system by means of temperature reassignment Using this method all of the velocities in the system are periodically reassigned so 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 reassignFreg 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
186. to a set of atoms to alter or rearrange part of the molecular structure For more information on VMD see http www ks uiuc edu Research vmd e Load Balancing An important factor in parallel applications is the equal distribution of computational load among the processors In parallel molecular simulation a spatial decomposition that evenly distributes the computational load causes the region of space mapped to each processor to become very irregular hard to compute and difficult to generalize to the evaluation of many different types of forces NAMD addresses this problem by using a simple uniform spatial decomposition where the entire model is split into uniform cubes of space called patches An initial load balancer assigns patches and the calculation of interactions among the atoms within them to processors such that the computational load is balanced as much as possible During the simulation an incremental load balancer monitors the load and performs necessary adjustments 1 3 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 sugge
187. toms 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 6 12 Pressure Profile Calculations NAMD supports the calculation of lateral pressure profiles as a function of the z coordinate in the system The algorithm is based on that of Lindahl and Edholm JCP 2000 with modifications to enable Ewald sums based on Sonne et al JCP 122 2005 The simulation space is partitioned into slabs and half the virial due to the interaction between two particles is assigned to each of the slabs containing the particles This amounts to employing the Harasima contour rather than the Irving Kirkwood contour as was done in NAMD 2 5 The diagonal components of the pressure tensor for each slab averaged over 107 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 in teractions 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 contributions to the Ewald sum were always computed offline If the simulations are per
188. topology file lt chain gt Single character chain identifier 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 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 d
189. tribution to enhanced atoms If used alone enhanced atoms would move faster than normal atoms and hence a smaller timestep would be required lesFile lt PDB file containing LES flags gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to specify the LES image number of each atom If this parameter is not specified then the PDB file containing initial coordinates specified by coordinates is used 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 6 11 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 A 106 For trajectory analysis the recommended way to use this set of options is to
190. ture 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 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 d
191. ua tion 8 the wealth of information available in fepOutFile may be utilized profitably to explore different routes towards the estimation of AA As commented on previously TI may constitute one such route The simple overlap sampling SOS represents an interesting alternative that combines advantageously forward and reverse transformations to improve convergence and accuracy of the calculation 20 The linear scaling of the Hamiltonian highlighted in equation 10 obviates the need for explicit simulation of the reverse transformation because Mi Ait P X Bai Mi HOG Poi Ait JOO H x Pz Ait2 H X Pz Ai 1 11 104 The free energy difference between states A and A 1 may then be expressed as nao exp E Hix pai Asst Hee pai ADIY E exp HC pes Ai HC pai Ar Y i exp 5 H x Pz Aiy1 H X Pz xp 2 i eae exp 8 L H x Pa i 2 H X Pz as 2 Ai 2 i 1 i 6 10 Locally Enhanced Sampling Locally enhanced sampling LES 25 26 27 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 6
192. ues 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 e mollyTolerance lt allowable error for MOLLY gt Acceptable Values positive decimal Default Value 0 00001 Description Convergence criterion for MOLLY algorithm e mollyIterations lt maximum MOLLY iterations gt Acceptable Values positive integer Default Value 100 Description Maximum number of iterations for MOLLY algorithm 55 6 Additional Simulation Parameters 6 1 Constraints and Restraints 6 1 1 Harmonic constraint parameters The following describes the parameters for the harmonic constraints feature of NAMD Actually this feature should be referred to as harmonic restraints rather than constraints but 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
193. ues position Description Location around which sphere is centered sphericalBCr1 lt radius for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect This distance is a radius from the center 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 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 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 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 sphericalBCexp2 lt exponent for second potential gt Acceptable Values positive even int
194. ult 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 seed lt random number seed gt Acceptable Values positive integer Default Value pseudo random value based on current UNIX clock time Description Number used to seed the random number generator if temperature or langevin is selected This can be used so that consecutive simulations produce the same 49 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 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 co
195. using a modified Nos Hoover method in which Langevin dynamics is used to control fluctuations in the barostat This method should be combined with a method of temperature control such as Langevin dynamics in order to simulate the NPT ensemble The Langevin piston Nose Hoover method in NAMD is a combination of the Nose Hoover constant pressure method as described in GJ Martyna DJ Tobias and ML Klein Constant pressure molecular dynamics algorithms J Chem Phys 101 5 1994 with piston fluctuation control implemented using Langevin dynamics as in SE Feller Y Zhang RW Pastor and BR Brooks Constant pressure molecular dynamics simulation The Langevin piston method J Chem Phys 103 11 1995 67 The equations of motion are r p mt er pP F e p gp R Vv 3Ve e 3V W P Po gee Re W Wo 3N RD lt R gt 2mgkT h Tr oscillationperiod lt R gt 2WgekT h 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 Descrip
196. ut 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 e nextatom Sets the internal counter to a new atom and return 1 or return 0 if all atoms have been processed this may even happen the first call This should be called as the condition of a while loop i e while nextatom to iterate over all atoms One one atom may be accessed at a time e dropatom Excludes the current atom from future iterations on this processor until cleardrops is called Use this to eliminate extra work when an atom will not be needed for future force calculations If the atom migrates to another processor it may reappear so this call should be used only as an optimization e cleardrops All available atoms will be iterated over by nextatom as if dropatom had never been called e getcoord Returns a list x y z of the position of the current atom wrapped in the periodic cell if there is one in the current wrapping mode as specified by wrapmode e getcell Returns a list of 1 4 vectors containing the cell origin center and as many basis vectors as exist i e ox oy oz ax ay az bx by bz cx cy cz It is more efficient to set the wrapping mode than to do periodic image calculations in Tcl e getmass Returns the mass of the current atom e getcharge Retu
197. ween NAMD and X PLOR configuration param eters NAMD was designed to provide many of the same molecular dynamics functions that X PLOR provides As such there are many similarities between the types of parameters that must be passed to both X PLOR and NAMD This section describes relations between similar NAMD and X PLOR parameters e NAMD Parameter cutoff X PLOR Parameter CTOFNB When full electrostatics are not in use within NAMD these parameters have exactly the same meaning the distance at which electrostatic and van der Waals forces are truncated When full electrostatics are in use within NAMD the meaning is still very similar The van der Waals force is still truncated at the specified distance and the electrostatic force is still computed at every timestep for interactions within the specified distance However the NAMD integration uses multiple time stepping to compute electrostatic force interactions beyond this distance every stepspercycle timesteps e NAMD Parameter vdwswitchdist X PLOR Parameter CTONNB Distance at which the van der Waals switching function becomes active e NAMD Parameter pairlistdist X PLOR Parameter CUTNb Distance within which interaction pairs will be 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 Pa
198. 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 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 dist
199. xed restraints 1 restrain the position of the ca atom of residue 0 2 restrain the distance between the ca s of residues 0 and 10 to 5 2A 3 restrain the angle between the ca s of residues 0 10 20 to 90 4 restrain the dihedral angle between the ca s of residues 0 10 20 30 to 180 5 restrain the angle between the centers of mass of residues 0 10 20 to 90 urestraint posi insulin 0 ca kf 20 ref 10 11 11 dist insulin 0 ca insulin 10 ca kf 20 ref 5 2 angle insulin 0 ca insulin 10 ca insulin 20 ca kf 20 ref 90 dihe insulin 0 ca insulin 10 ca insulin 20 ca insulin 30 ca barr 20 ref 180 angle insulin 0 insulin 10 insulin 20 kf 20 ref 90 1 restrain the center of mass of three atoms of residue 0 2 restrain the distance between the COM of 3 atoms of residue 0 to the COM of 3 atoms of residue 10 3 restrain the dihedral angle of 10 11 12 15 16 17 18 20 22 30 31 32 34 35 to 90 ca of 10 to 12 ca cb cg of 15 to 18 all atoms of 20 and 22 ca of 30 31 32 34 all atoms of 35 urestraint posi group insulin 0 ca insulin 0 cb insulin 0 cg kf 20 ref 10 11 11 dist group insulin 0 ca insulin 0 cb insulin 0 cg group insulin 10 ca insulin 10 cb insulin 10 cg kf 20 ref 6 2 dihe group ca insulin 10 to insulin 12 group ca cb cg insulin 15 to insulin 18 group insulin
200. y 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 50 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 5 2 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 interactions as detailed in Section 5 2 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
201. y segid is specified all atoms from that segment will be removed from the structure If both segid and resid are specified all atoms from just that residue will be removed If segid resid and atom name are all specified just a single atom will be removed Arguments lt segid gt Name of segment lt resid gt Name of residue optional lt atom name gt Name of atom optional Context After all segments have been built and patched 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
202. youtput 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 restarts 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 o
203. ypically this would be chosen equal to or smaller than the piston period such as 100 fs e LangevinPistonTemp lt noise temperature K gt Acceptable Values positive decimal 68 Description Specifies barostat noise temperature for Langevin piston method This should be set equal to the target temperature for the chosen method of temperature control e 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 e 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 e 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
204. za E Vips yo ya it ta t0 j 0 0 Gradient for forcing position restraint E K5 2 R Pref Tref ATi 1 A T 1 2 dE dA Kpx Ce ares Yi vref zi 2re1 x 2 2 2 71 2 1 2 ti tres Yi Yref z ret x 2 i Eres o 21 2 yi Yref Yo Y1 2 zi Zref 20 21 dE dA Kp x 2 Tres o 11 Yi Yref Yo Y1 zi Zref zo 21 Gradient for forcing stretch restraint 91 E Ky 2 di dyes dref Ad 1 A do dE dA Ks x di dref x do di Gradient for forcing bend restraint E K 5 2 0 ref Oro AO 1 A 00 dE dA K x 6 Ores x 00 01 Gradient for forcing dihedral restraint E Ep 2 1 COS Xi E Xref Xref Ax1 1 A xo dE d Eo 2 x sin xi Xref x Xxo X1 6 8 Adaptive Biasing Force Calculations This feature has been contributed to NAMD by the following authors J r me H nin and Christophe Chipot Equipe de dynamique des assemblages membranaires Institut nanc ien de chimie mol culaire UMR CNRS UHP 1565 Universit Henri Poincar BP 239 54506 Vandoeuvre les Nancy cedex France 2005 CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE 6 8 1 Introduction and theoretical background Strictly speaking a potential of mean force PMF is the reversible work supplied to the system to bring two solvated particles or ense

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