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1. Unshifted Shifted S 6 amp 1 1 1 j 1 j 1 i jt 1 1 1 1 4 5 6 7 0 1 2 3 4 5 6 7 0 1 2 3 Grid index Figure 5 Graph showing a slice of a ramp potential with eight grid points along the axis and a periodic cell size which just contains the grid The Unshifted case shows how the pontential is not smooth when mgridforcevoff is not specified or set to zero The Shifted potential shows the grid that results when mgridfocevoff is set so that the wrapped potential is offset so that the potential has constant slope at the periodic boundaries value for the force constant k in the PDB file 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 direction 9 5 Rotating Constraints The constraints parameters are specified in the same manner as for usual static harmonic c
2. atoms 1 2 3 5 C 1 0 p 1 colvar d d d i 113 harmonic restraint distance d Yo K d d t w atoms 7 8 10 c c t w C 1 0 p 1 coord num coord atoms 1 10 11 20 radius 6 A colvar c coord histogram alpha c colvar alpha alpha alpha helix alpha residues 1 10 Figure 6 Example of a collective variables colvar configuration The colvar d is defined as the difference between two distances each calculated between the centers of mass of two atom groups The second colvar c holds the coordination number i e the number of contacts within a radius of 6 A between two groups The third colvar alpha measures the degree of a helicity of the protein segment between residues 1 and 10 A moving harmonic restraint is applied to the colvars d and c each rescaled by means of width parameters wg and we the centers of the restraint do and co evolve with the simulation time t The joint histogram of alpha and c is also recorded on the fly e colvars lt Enable the collective variables module gt Acceptable Values boolean Default Value off Description If this flag is on the collective variables module within NAMD is enabled the module requires a separate configuration file to be provided with colvarsConfig e colvarsConfig lt Configuration file f
3. 24 25 26 27 28 retpjs Tij Te pPjst raj Ps r 1_ jy T22 Br2r2 2 a MA rerij 0js i5 Tij 3 5 7 9 11 p3 Pp pi PS P dat 60 8c 10d 120 _ _ NR mna O ij ij 1 2 aj oe 2 2 SEE a Pal yte is 1 In i Lis 29 Orij rij r303 2ri Tit Pie 2 2 2 21 59 2 2 2 tv 2 Teas relojes Arise P75 007s 1 Pio g 2070 2r2 po rij ojs ri Tij pjs 2 2 vol pis ri s 1 Ip Pisa his 2 2 oa 3 2 rlr 2rij Tig TPis VI Other variables referenced in the above GB equations are rij distance between atoms i and j calculated from atom coordinates k debye screening length calculated from ion concentration k 4 ete KT 10 for 0 1 M monovalent salt s dielectric constant of solvent p dielectric constant of protein a Born radius of atom 7 pi intrinsic radius of atom i taken from Bondi 7 po intrinsic radius offset p 0 09 A by default 50 Pio Pi PO Pis Pio Sij Sij atom radius scaling factor 28 60 ke Coulomb s constant 332 063711 kcal A e reo 16 B y 0 8 0 2 91 or 1 0 0 8 4 85 50 6 2 3 Phase Calculation The GBIS algorithm requires three phases of calculation with each phase containing an iteration over all atom pairs with the cutoff In phase 1 the screening of atom pairs is summed at the a 2 OEG eer conclusion of phase 1 the Born radii are calculate
4. 46 47 M lannuzzi A Laio and M Parrinello Efficient exploration of reactive potential energy surfaces using car parrinello molecular dynamics Phys Rev Lett 90 23 238302 2003 W Jiang D Hardy J Phillips A MacKerell K Schulten and B Roux High performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD J Phys Chem Lett 2 87 92 2011 P M King Free energy via molecular simulation A primer In W F Van Gunsteren P K Weiner and A J Wilkinson editors Computer simulation of biomolecular systems Theoretical and experimental applications volume 2 pages 267 314 ESCOM Leiden 1993 J G Kirkwood Statistical 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 E A Koopman and C P Lowe Advantages of a Lowe Andersen thermostat in molecular dynamics simulations J Chem Phys 124 204103 2006 A Laio and M Parrinello Escaping free energy minima Proc Natl Acad Sci USA 99 20 12562 12566 2002 G Lamoureux E Harder I V Vorobyov B Roux and A D MacKerell A polarizable model of water for molecular dynamics simulations of biomolecules Chem Phys Lett 418 1 3 245 249 2006 G Lamoureux and B Roux Modeling induced polarization with classical Drude oscillators Theory
5. triplet of positive decimals Default Value 4 0 4 0 4 0 Description The three components of this vector define three different cutoffs dy for each direction This option is mutually exclusive with cutoff e group2CenterOnly lt coordNum Use only group2 s center of mass gt Acceptable Values boolean Default Value off Description If this option is on only contacts between the atoms in group1 and the center of mass of group2 are calculated By default the sum extends over all pairs of atoms in group1 and group2 119 This component returns a dimensionless number which ranges from approximately 0 all inter atomic distances much larger than the cutoff to Ngroup1 Ngroup2 all distances within the cutoff or Ngroupi if group2CenterOnly is used For performance reasons at least one of group1 and group2 should be of limited size unless group2CenterOnly is used because the cost of the loop over all pairs grows as Ngroup1 Ngroup2 Component selfCoordNum coordination number between atoms within a group The selfCoordNum block defines a coordination number in much the same way as coordNum but the function is summed over atom pairs within group1 i groupl j gt i xi e x do The keywords accepted by selfCoordNum are a subset of those accepted by coordNum namely group1 here defining all of the atoms to be considered cutoff expNumer and expDenon This component returns a dimensionless number which
6. ee 18 NAMD Availability and Installation 18 1 How to obtainNAMD r coon eG ae ea a e A 18 2 Platforms on which NAMD will currently run 04 18 3 InstallingsNAMD it io Qe see Re de POG Ae Roe Ee a ES 18 4 Compiling NAMD 2 s casi A glee ee ee dle ek eae ad eke 18 5 Documentation ss 4 4 erat aoe FoR og ee a hk bee ae hoe gon SOURS References Index 165 165 165 165 166 168 168 169 173 175 180 180 180 180 181 182 183 183 184 184 184 186 186 188 188 188 188 188 189 190 195 List of Figures oOorwnr 10 11 Graph of van der Waals potential with and without switching Graph of electrostatic potential with and without shifting function Graph of electrostatic split between short and long range forces Example of cutoff and pairlist distance uses 2 2 ee ee ee Graph showing a slice of a ramp potential showing the effect of mgridforcevoff Example of a collective variables colvar configuration The colvar d is defined as the difference between two distances each calculated between the centers of mass of two atom groups The second colvar c holds the coordination number i e the number of contacts within a radius of 6 A between two groups The third colvar alpha measures the degree of a helicity of the protein segment between residues 1 and 10 A moving harmonic restraint is applied to the colvars d and c
7. group main pathfix tmp _mnt host alphai host alpha2 There are many other options to charmrun and for the nodelist file These are documented at in the Charm Installation and Usage Manual available at http charm cs uiuc edu manuals and a list of available charmrun options is available by running charmrun without arguments If your workstation cluster is controlled by a queueing system you will need build a nodelist file in your job script For example if your queueing system provides a HOST_FILE environment variable set NODES cat HOST_FILE set NODELIST TMPDIR namd2 nodelist echo group main gt NODELIST foreach node nodes echo host node gt gt NODELIST end NUMPROCS 2 NODES charmrun namd2 p NUMPROCS nodelist NODELIST lt configfile gt Note that NUMPROCS is twice the number of nodes in this example This is the case for dual processor machines For single processor machines you would not multiply 4NODES by two Note that these example scripts and the setenv command are for the csh or tcsh shells They must be translated to work with sh or bash 17 5 Shared Memory and Network Based Parallelism SMP Builds The Linux x86_64 ibverbs smp and Solaris x86_64 smp released binaries are based on smp builds of Charm that can be used with multiple threads on either a single machine like a multicore build or across a network SMP builds combine multiple worker threads and an extra communicati
8. lambda Figure 10 Sample TI data log Y against A The blue shaded area shows the integral with fine sampling close to the end point The red area shows the difference when values are more sparse In this example insufficient sampling before A 0 1 can result in a large overestimation of the integral Beyond 0 2 sparser sampling is justified as dE dA is not changing quickly Part 1 0 5748 6 3452 6 9200 Part 2 0 5391 4 9387 5 4778 Mea aaa aaa ale Subtotall 0 6048 0 3293 Total deltaG for transition lambda 0 gt 1 12 3978 sense may encourage interpretations along the lines of the free energy for switching on the van der Waals context of the simulation setup and parameters used in this case and is not informative in a broader interactions for the atoms of partition 1 was 6 35kcal mol This is only correct in the very narrow The choice of values will depend on the application but in general it is important to examine the shape of the curve to ensure that sampling is adequate to give a good estimate of the integral In system see Figure 10 particular it will be necessary to sample more finely towards the end points in order to accurately account for the strong repulsive van der Waals forces encountered when inserting particles into a 152 12 Accelerated Sampling Methods 12 1 Accelerated Molecular Dynamics Accelerated molecular dynamics aMD 26 is an enhanced sampling
9. 2 2 2 Tcl scripting interface and features When compiled with Tcl all released binaries the config file is parsed by Tcl in a fully backwards compatible manner with the added bonus that any Tcl command may also be used This alone allows e the source command to include other files works w o Tcl too e the print command to display messages puts is broken sorry e environment variables through the env array Senv USER and e user defined variables set base sim23 dedfile base dcd Additional features include e The callback command takes a 2 parameter Tcl procedure which is then called with a list of labels and a list of values during every timestep allowing analysis formatting whatever e The run command takes a number of steps to run overriding the now optional numsteps parameter which defaults to 0 and can be called repeatedly You can run 0 just to get energies e The minimize command is similar to run and performs minimization for the specified number of force evaluations e The output command takes an output file basename and causes coor vel and xsc files to be written with that name Alternatively output withforces and output onlyforces will write a force file either in addition to or instead of the regular files 4 bj e Between run commands the reassignTemp rescaleTemp and langevinTemp parame ters can be changed
10. 2 T3 T4 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 aid1 112 set aid2 123 set aid3 117 set aid4 115 The spring constant for the harmonic constraint set k 3 0 addatom aidi addatom aid2 addatom aid3 addatom aid4 set PI 3 1416 proc calcforces 100 global aidi aid2 aid3 aid4 k PI loadcoords p Calculate the current dihedral set phi getdihedral p aid1 p aid2 p aid3 p aid4 Change to radian set phi expr phi PI 180 optional Add this constraining energy to MISC in the energy output addenergy expr k phi phi 2 0 Calculate the force along the dihedral according to the harmonic constraint set force expr k phi Calculate the gradients foreach g1 g2 g3 g4 dihedralgrad p aid1 p aid2 p 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 9 11 Tcl Boundary Forces While the tclForces interface described above is very flexible it is only efficient for
11. AMBER format PARM file and coordinate file can be read by NAMD which allows one to use AMBER force field to carry out all types of simulations that NAMD has supported NAMD can read PARM files in either the format used in AMBER 6 or the new format defined in AMBER 7 The output of the simulation restart file DCD file etc will still be in traditional format that has been used in NAMD e amber lt use AMBER format force field gt Acceptable Values yes or no Default Value no Description If amber is set to on then parmfile must be defined and structure and parameters should not be defined e parmfile lt AMBER format PARM file gt Acceptable Values UNIX filename Description This file contains complete topology and parameter information of the system e ambercoor lt AMBER format coordinate file gt Acceptable Values UNIX filename Description This file contains the coordinates of all the atoms Note that coordinates can also be used for PDB format coordinate file When amber is set to on either ambercoor or coordinates must be defined but not both e readexclusions lt Read exclusions from PARM file gt Acceptable Values yes or no Default Value 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 th
12. Acceptable Values UNIX filename Description The file to write out restart information for adaptive tempering adaptTempRestartFreq lt steps between writing restart file gt Acceptable Values Positive integer Description Frequency of writing restart file adaptTempLangevin lt send temperature updates to langevin thermostat gt Acceptable Values on or off Default Value on Description Setting this to on will cause the langevin thermostat to use the updated tem peratures from adaptive tempering Note that either one of adaptTempLangevin or adapt TempRescaling have to be on adaptTempRescaling lt send temperature to velocity rescaling thermostat gt Acceptable Values on or off Default Value on Description Setting this to on will cause the veloctiy rescaling thermostat to use the updated temperatures from adaptive tempering Note that either one of adaptTempLangevin or adaptTempRescaling have to be on adaptTempOutFreq lt steps between printing adaptive tempering output gt Acceptable Values Positive integers Default Value 10 Description The number of timesteps between printing adaptive tempering output to the log file adaptTempFirstStep lt step to start adaptive tempering gt Acceptable Values Non negative integers Default Value 0 Description The first timestep from which adaptive tempering will be run adaptTempLastStep lt step to stop adaptive tempering gt Acceptable Values Positive int
13. NAMD User s Guide Version 2 9b3 M Bhandarkar A Bhatele E Bohm R Brunner F Buelens C Chipot A Dalke S Dixit G Fiorin P Freddolino P Grayson J Gullingsrud A Gursoy D Hardy C Harrison J H nin W Humphrey D Hurwitz N Krawetz S Kumar D Kunzman J Lai C Lee R McGreevy C Mei M Nelson J Phillips O Sarood A Shinozaki D Tanner D Wells G Zheng F Zhu April 5 2012 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 9b3 Authors M Bhandarkar A Bhatele E Bohm R Brunner F Buelens C Chipot A Dalke S Dixit G Fiorin P Freddolino P Grayson J Gullingsrud A Gursoy D Hardy C Harrison J H nin W Humphrey D Hurwitz N Krawetz S Kumar D Kunzman J Lai C Lee R McGreevy C Mei M Nelson J Phillips O Sarood A Shinozaki D Tanner D Wells G Zheng F Zhu Theoretical Biophysics Group Beckman Institute University of Illinois 1995 2011 The Board of Trustees of the University of Illinois All Rights Reserved NAMD Molecular Dynamics Soft
14. 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 ON ACCOUNT OF OR ARISING FROM THIS AGREEMENT OR USE OF THE SOFTWARE AND OR ASSOCIATED MATERIALS 4 Licensee understands the Software is proprietary to Illinois Licensee agrees to take all reasonable steps to insure that the Software is protected and secured from unauthorized disclosure use or release and will treat it with at least the same level of care as Licensee would use to protect and secure its own proprietary computer programs and or information but using no less than a reasonable standard of care Licensee agrees to provide the Software only to any other person or entity who has registered with Illinois If licensee is not registering as an individual but as an institution or corporation each member of the institution or corporation who has access to or uses Software must understand and agree to the terms of this license If Licensee becomes aware of any unauthorized licensing copying or use of the Software Licensee shall promptly notify Illinois in writing Licensee expressly agrees to use the Software only in the manner and for the specific uses authorized i
15. initial config coordinates alanin pdb temperature 300K seed 12345 periodic cell cellBasisVector1l 33 00 0 cellBasisVector2 0 32 0 0 cellBasisVector3 0 0 32 5 output params outputname tmp alanin binaryoutput no DcDfreq 10 restartfreq 100 integrator par timestep force field pa structure parameters exclude 1 4scaling switching switchdist cutoff pairlistdist stepspercycle ams 1 0 rams alanin psf alanin params scaled1 4 1 0 on 8 0 12 0 13 5 20 176 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 32 177 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 a
16. which calculates the function 1 d do 1 d do where do is the cutoff distance and n and m are exponents that can control its long range behavior and stiffness 33 This function is summed over all pairs of atoms in group1 and group2 fi 1 C group1 group2 Ds D 1 1Egroup1 Egroup2 xi x31 do x x do 37 This colvar component accepts the same keywords as distance group1 and group2 In addition to them it recognizes the following keywords e cutoff lt coordNum Interaction distance A gt Acceptable Values positive decimal Default Value 4 0 Description This number defines the switching distance to define an interatomic contact for d lt do the switching function 1 d do 1 d do is close to 1 at d dy it has a value of n m 1 2 with the default n and m and at d gt dy it goes to zero approximately like d Hence for a proper behavior m must be larger than n e expNumer lt coordNum Numerator exponent gt Acceptable Values positive even integer Default Value 6 Description This number defines the n exponent for the switching function e expDenom lt coordNum Denominator exponent gt Acceptable Values positive even integer Default Value 12 Description This number defines the m exponent for the switching function e cutoff3 lt coordNum Reference distance vector A gt Acceptable Values x y z
17. Description The binary file containing initial velocities for all atoms in the simulation A binary velocity file is created as output from NAMD by activating the binaryrestart or binaryoutput options The binvelocities option should be used as an alternative to velocities Either the temperature or the velocities binvelocities option must be defined to determine an initial set of velocities Both options cannot be used together e bincoordinates lt binary coordinate restart file gt Acceptable Values UNIX filename Description The binary restart file containing initial position coordinate data A binary coordinate restart file is created as output from NAMD by activating the binaryrestart or binaryoutput options Note that in the current implementation at least the bincoordinates option must be used in addition to the coordinates option but the positions specified by coordinates will then be ignored e cwd lt default directory gt Acceptable Values UNIX directory name Description The default directory for input and output files If a value is given all filenames that do not begin with a are assumed to be in this directory For example if cwd is set to scr 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 giv
18. FFTW_NAMD_version_platform txt 48 Description File where FFTW wisdom is read and saved If you only run on one platform this may be useful to reduce startup times for all runs The default is likely sufficient as it is version and platform specific 5 2 5 Full direct parameters The direct computation of electrostatics is not intended to be used during real calculations but rather as a testing or comparison measure Because of the O N computational complexity for performing direct calculations this is much slower than using PME to compute full electrostatics for large systems In the case of periodic boundary conditions the nearest image convention is used rather than a full Ewald sum e FullDirect lt calculate full electrostatics directly gt Acceptable Values yes or no Default Value no Description Specifies whether or not direct computation of full electrostatics should be performed 5 2 6 Tabulated nonbonded interaction parameters In order to support coarse grained models and semiconductor force fields the tabulated energies feature replaces the normal van der Waals potential for specified pairs of atom types with one interpolated from user supplied energy tables The electrostatic potential is not altered Pairs of atom types to which the modified interactions apply are specified in a CHARMM parameter file by an NBTABLE section consisting of lines with two atom types and a corresponding interaction type name For exampl
19. Force constant for the first harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center e sphericalBCexp1 lt exponent for first potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for first boundary potential The only likely values to use are 2 and 4 e sphericalBCr2 lt radius for second boundary condition A gt Acceptable Values positive decimal Description Distance at which the second potential of the boundary conditions takes effect This distance is a radius from the center If this parameter is defined then spericalBCk2 must also be defined e sphericalBCk2 lt force constant for second potential gt Acceptable Values non zero decimal Description Force constant for the second harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center e sphericalBCexp2 lt exponent for second potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for second boundary potential The only likely values to use are 2 and 4 7 1 3 Cylindrical harmonic boundary conditions NAMD provides cylindrical harmonic boundary conditions These boundary conditions can consist of a single potential or a combination of two potentials The following parameters are used to define these boundary conditions e cylindricalBC lt use
20. The Win64 MPI version of NAMD runs on Windows HPC Server and should be launched as you would any other MPI program 17 3 Linux Clusters with InfiniBand or Other High Performance Networks Charm provides a special ibverbs network layer that uses InfiniBand networks directly through the OpenFabrics OFED ibverbs library This avoids efficiency and portability issues associated with MPI Look for pre built ibverbs NAMD binaries or specify ibverbs when building Charm Writing batch job scripts to run charmrun in a queueing system can be challenging Since most clusters provide directions for using mpiexec to launch MPI jobs charmrun provides a mpiexec option to use mpiexec to launch non MPI binaries If mpiexec np procs is not sufficient to launch jobs on your cluster you will need to write an executable mympiexec script like the following from TACC 180 bin csh shift shift exec ibrun x The job is then launched with full paths where needed as charmrun p lt procs gt mpiexec remote shell mympiexec namd2 lt configfile gt For workstation clusters and other massively parallel machines with special high performance networking NAMD uses the system provided MPI library with a few exceptions and standard system tools such as mpirun are used to launch jobs 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
21. Through simulations at progressive values of alchLambda and alchLambda2 the total free energy difference may be determined e alchEquilSteps lt Number of equilibration steps in a window prior to data collection gt Acceptable Values positive integer less than numSteps or run Default Value 0 Description In each window alchEquilSteps steps of equilibration can be performed before ensemble averaging is initiated The output also contains the data gathered during equilibration and is meant for analysis of convergence properties of the alchemical free energy calculation e alchFile lt pdb file with perturbation flags gt Acceptable Values filename Default Value coordinates Description pdb file to be used for indicating the status of all atoms pertaining to the 146 system with respect to the alchemical transformation If this parameter is not declared specifically then the pdb file specified by coordinates is utilized for this information alchCol lt Column in the alchFile that carries the perturbation flag gt Acceptable Values X Y Z O or B Default Value B Description Column of the pdb file to use for retrieving the status of each atom i e a flag that indicates which atom will be perturbed in the course of the alchemical transformation A value of 1 in the specified column indicates that the atom will vanish as A moves from 0 to 1 whereas a value of 1 indicates that it will grow alchOutFreq lt Frequency of free
22. i xidel j yidel k zldel y i j k yorg i x2del j y2del k z2del z i j k zorg i x3del j y3del k z3del Grid data follows with three values per line ordered z fast y mediun and x slow Exactly xn yn zn values should be given Grid data is then terminated with a field object Note Other features of the DX file format are not handled by this code HH HH H HH FH H HOF OH OF object 1 class gridpositions counts xn yn zn origin xorg yorg zorg delta xidel yidel zidel delta x2del y2del z2del delta x3del y3del z3del object 2 class gridconnections counts xn yn zn object 3 class array type double rank O items xn yn zn data follows f1 12 f3 f4 f5 6 object 4 class field component positions value 1 component connections value 2 component data value 3 Each dimension of the grid may be specified as continuous or not If the grid is not continuous in a particular dimension the potential grid is padded with one border slices on each non continuous face of the grid and border grid values are computed so that the force felt by an atom outside the 86 grid goes to zero If the grid is continuous along a particular dimension atoms outside the grid are affected by a potential that is interpolated from the grid and its corresponding periodic image along that dimension To calculate the force on an atom due to the grid the atom s coordinates are transformed according to the current basis
23. langevinHydrogen parameter 73 LangevinPiston parameter 15 79 LangevinPistonDecay parameter 15 79 LangevinPistonPeriod parameter 15 79 LangevinPistonTarget parameter 15 79 LangevinPistonTemp parameter 15 80 langevinTemp parameter 15 73 last psfgen command 36 les parameter 158 lesCol parameter 159 lesFactor parameter 158 lesFile parameter 159 lesReduceMass parameter 159 lesReduceTemp parameter 158 limitdist parameter 47 LJcorrection parameter 47 longSplitting parameter 72 loweAndersen parameter 76 loweAndersenCutoff parameter 76 loweAndersenRate parameter 76 loweAndersenTemp parameter 76 lowerBoundary parameter 111 lowerWall parameter 112 lower WallConstant parameter 112 main parameter 117 margin parameter 83 margin violations 81 martiniDielAllow parameter 54 martiniSwitching parameter 54 maximumMove parameter 69 measure command 16 mergeCrossterms parameter 23 mgridforce parameter 87 megridforcechargecol parameter 88 megridforcecol parameter 88 megridforcecontl parameter 88 megridforcecont2 parameter 89 meridforcecont3 parameter 89 meridforcefile parameter 88 meridforcelite parameter 89 meridforcepotfile parameter 88 meridforcescale parameter 88 meridforcevoff parameter 89 meridforcevolts parameter 88 minBabyStep parameter 69 minimization parameter 69 minimize command 15 minLineGoal parameter 69 minTinyStep parameter 69 MISC energy 23 molly parameter 72 m
24. the switching functions could be turned off by specifying switching off in NAMD configuration file 6 NAMD and AMBER may have different default values for some parameters e g the tolerance of SHAKE One should check other sections of this manual for accurate descriptions of the NAMD options Following are two examples of the NAMD configuration file to read AMBER force field and carry out simulation They may help users to select proper NAMD options for AMBER force field For the convenience of AMBER users the AMBER 6 sander input files are given in the left for comparison which would accomplish similar tasks in AMBER Example 1 Non periodic boundary system cutoff simulation AMBER NAMD TITLE gcntrl ntb 0 igb 2 non periodic use cutoff for non bond nstlim 1000 numsteps 1000 Num of total steps ntpr 50 outputEnergies 50 Energy output frequency ntwr 50 restartfreq 50 Restart file frequency ntwx 100 DCDfreq 100 Trajectory file frequency dt 0 001 timestep 1 in unit of fs This is default tempi 0 temperature O Initial temp for velocity assignment cut 10 cutoff 10 switching off Turn off the switching functions scee 1 2 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 Example 2 Pe
25. 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 vdwGeometricSigma lt use geometric mean to combine L J sigmas gt Acceptable Values yes or no 46 Default Value no Description Use geometric mean as required by OPLS rather than traditional arithmetic mean when combining Lennard Jones sigma parameters for different atom types e limitdist lt maximum distance between pairs for limiting interaction strength A gt Acceptable Values non negative decimal Default Value 0 Description The electrostatic and van der Waals potential functions diverge as the distance between two atoms approaches zero The potential for atoms closer than limitdist is instead treated as ar c with parameters chosen to match the force and potential at limitdist This option should primarily be useful for alchemical free energy perturbation calculations since it makes the process of creating and destroying atoms far less drastic energetically The larger the value of limitdist the more the maximum force between atoms will be reduced In order to not al
26. 00000004 o Pressure Control taa Ae Grae ehh Rook hy Boge Reed AR eS 7 5 1 Berendsen pressure bath coupling 2 220 4 7 5 2 Nos Hoover Langevin piston pressure control 0200 Performance Tuning 8 1 Non bonded interaction distance testing 2 0 2 a eee ee eee 59 59 59 59 59 62 63 65 65 65 66 67 68 68 69 69 69 70 71 71 73 73 74 74 75 75 76 TT 78 81 9 User Defined Forces 9 1 Constant Forces 9 2 External Electric Field 0 00 0 000000 a a e a ee 9 3 Grid Forces 9 4 Moving Constraints 9 5 Rotating Constraints 9 6 Symmetry Restraints 9 7 Targeted Molecular Dynamics TMD 9 8 Steered Molecular Dynamics SMD o e e 9 9 Interactive Molecular Dynamics IMD AA GS 9 10 Tcl Forces and Analysis e 9 11 Tcl Boundary Forces 9 12 External Program Forces aooaa 10 Collective Variable based Calculations 10 1 General parameters and input output files 10 1 1 NAMI parameters ae od Ah Be ee a a a ee ee RO 10 1 2 Output files 10 1 3 Colvars module configuration file 02 20 0002 00 10 2 Declaring and using collective variables 2 a a ee 10 2 1 General collective variable options 0 000002 00s 10 2 2 Collective variable components 2 0 e 10 2 3 Linear and polynomial combinations of components
27. 1 2 set alchLambda2 value run 10000 3 run 10 000 MD steps This option is generally preferred to set up windows of diminishing widths as A 0 or 1 a way to circumvent end point singularities caused by appearing atoms that may clash with their 149 surroundings The following second input is proposed for the measuring via TI the free energy of a particle insertion alch On Enable alchemical simulation module alchType ti Set method to thermodynamic integration alchFile ion alch pdb PDB file with perturbation flags alchCol B Perturbation flags in Beta column alchOutfile ion ti out alchOutFreq 5 alchEquilSteps 5000 alchVdWShiftCoeff 1 Enable soft core vdW potential alchElecLambdaStart 0 1 Introduce electrostatics for lambda gt 0 1 alchLambda 0 run 10000 alchLambda 0 00001 run 10000 alchLambda 0 0001 run 10000 alchLambda 0 001 run 10000 alchLambda 0 01 run 10000 set Lambda 0 1 while Lambda lt 0 9 4 alchLambda Lambda run 10000 set Lambda expr Lambda 0 1 alchLambda 0 99 run 10000 alchLambda 0 999 run 10000 alchLambda 0 9999 run 10000 alchLambda 0 99999 run 10000 alchLambda 1 run 10000 Robust sampling of the free energy of particle insertion is enabled by the use of soft core van der Waals scaling with the alchVdWShiftCoeff parameter delayed introduction of electrostatics with a non zero alchElecLambdaStart value and very gradual scaling of A towards its end points
28. 150 11 4 Description of a free energy calculation output 11 4 1 Free Energy Perturbation When running FEP the alchOutFile contains electrostatic and van der Waals energy data calcu lated for alchLambda and alchLambda2 written every alchOutFreq steps The column dE is the energy difference of the single configuration dE_avg and dG are the instantaneous ensemble average of the energy and the calculated free energy at the time step specified in column 2 respectively The temperature is specified in the penultimate column Upon completion of alchEquilSteps steps the calculation of dE_avg and dG is restarted The accumulated net free energy change is written at each lambda value and at the end of the simulation Whereas the FEP module of NAMD supplies free energy differences determined from equa tion 56 the wealth of information available in alchOutFile may be utilized profitably to explore different routes towards the estimation of AA Both BAR and SOS methods which combine advantageously direct and reverse transformations to improve convergence and accuracy of the calculation represent relevant alternatives to brute force application of the FEP formula 42 Within the SOS framework the free energy difference between states A and A 41 is expressed as exp E H x Pa Acta HS Pos anit exp 1 5 H x Po Ai H X Pz aanl and can be readily used with the statistical information provided by the forward and the backward
29. After an integration step of velocities and positions the position of the LP is updated based on the three guide atoms along with additional geometry parame ters that give displacement and in plane and out of plane angles See our research web page http www ks uiuc edu Research Drude for additional details and parallel performance re sults ol 5 4 1 Required input files No additional files are required by NAMD to use the Drude polarizable force field However it is presently beyond the capability of the Psfgen tool to generate the PSF file needed to perform a simulation using the Drude model For now CHARMM is needed to generate correct input files The CHARMM force field parameter files specific to the Drude model are required The PDB file must also include the Drude particles mass between 0 1 and 1 0 and the LPs mass 0 The Drude particles always immediately follow their parent atom The PSF file augments the atom section with additional columns that include the Thole and alpha parameters for the screened Coulomb interactions of Thole The PSF file also requires additional sections that list the LPs including their guide atoms and geometry parameters and list the anisotropic interaction terms including their parameters A Drude compatible PSF file is denoted by the keyword DRUDE given along the top line 5 4 2 Standard output The NAMD logging to standard output is extended to provide additional tempe
30. Colvar grid parameters e name lt colvar Name of this colvar gt Acceptable Values string Default Value colvar numeric id Description The name is an unique case sensitive string which allows the colvar module to identify this colvar unambiguously it is also used in the trajectory file to label to the columns corresponding to this colvar e width lt colvar Typical fluctuation amplitude or grid spacing gt Acceptable Values positive decimal Default Value 1 0 Description This number is a user provided estimate of the typical fluctuation ampli tude for this collective variable or conversely the typical width of a local free energy basin Typically twice the standard deviation during a very short simulation run can be used Bi asing methods use this parameter for different purposes harmonic restraints 10 3 3 use it to rescale the value of this colvar the histogram 10 3 4 and ABF biases 10 3 1 interpret it as the grid spacing in the direction of this variable and metadynamics 10 3 2 uses it to set the width of newly added hills This number is expressed in the same physical unit as the colvar value e lowerBoundary lt colvar Lower boundary of the colvar gt Acceptable Values decimal Description Defines the lowest possible value in the domain of values that this colvar can access It can either be the true lower physical boundary under which the variable is not defined by construction or an arbitrary va
31. FFTWWisdomFile parameter 48 first psfgen command 36 firsttimestep parameter 70 fixedAtoms parameter 16 56 fixedAtomsCol parameter 57 fixedAtomsFile parameter 56 fixedAtomsForces parameter 16 56 forceConstant parameter 139 forceDCDfile parameter 22 forceDCDfreq parameter 22 forceNoPBC parameter 117 118 FullDirect parameter 49 fullElectFrequency parameter 71 fullSamples parameter 133 GBIS parameter 63 GBISBeta parameter 63 GBISDelta parameter 63 GBISGamma parameter 63 GoCoordinates parameter 166 GoForcesOn parameter 165 GoMethod parameter 166 GoParameters parameter 165 GPRESSAVG 23 GPRESSURE 23 grocoorfile parameter 26 gromacs parameter 26 grotopfile parameter 26 groupl parameter 116 group2 parameter 116 group2CenterOnly parameter 119 guesscoord psfgen command 40 hBondCoeff parameter 124 hBondCutoff parameter 124 hBondExpDenom parameter 124 hBondExpNumer parameter 124 hgroupCutoff A parameter 83 hideJacobian parameter 133 hillWeight parameter 136 hillWidth parameter 137 historyFreq parameter 133 IMDfreq parameter 97 IMDignore parameter 98 IMDon parameter 97 IMDport parameter 97 IMDwait parameter 97 inputPrefix parameter 133 intrinsicRadiusOffset parameter 63 ionConcentration parameter 63 keepHills parameter 139 197 lambdaSchedule parameter 141 langevin parameter 73 langevinCol parameter 74 langevinDamping parameter 73 langevinFile parameter 73
32. RMS x t in other words only if the current RMSD fails to keep pace with the target value e TMDDiffRMSD lt Is double sided TMD active gt Acceptable Values on or off Default Value off Description Turns on the double sided TMD feature which targets the transition between two structures This is accomplished by modifying the TMD force such that the potential is based on the difference of RMSD s from the two structures Gee DRMS t DRMS t 32 where DRM S t is RMS1 t RMS2 2 RMS1 being the RMSD from structure 1 and RMS2 the RMSD from structure 2 The first structure is specified as normal in TMDFile and the second structure should be specified in TMDFile2 preserving any domain designations found in TMDFile e TMDFile2 lt Second structure file for double sided TMD gt Acceptable Values Path to PDB file Description PDB file defining the second structure of a double sided TMD This file should contain the same number of atoms as TMDFile along with the same domain designations if any are specified 9 8 Steered Molecular Dynamics SMD The SMD feature is independent from the harmonic constraints although it follows the same ideas In both SMD and harmonic constraints one specifies a PDB file which indicates which atoms are tagged as constrained The PDB file also gives initial coordinates for the constraint positions One also specifies such parameters as the force constant s for the constraints and the veloc
33. 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 NAMD and molecular dynamics simulations e e 12 Acknowledginents 2 2 3 3 dst ee ae A AR ea PE ee a es Getting Started 21 What is needed i 4 0 ao hoe hath bes AA Gen otha hot ae ee Bae 2 2 NAMD configuration fille 0 0 ee eee eee 2 2 1 Configuration parameter syntax s 2 2 ee ee 2 2 2 Tcl scripting interface and features o e 000020000048 2 2 3 Required NAMD configuration parameters e a Input and Output Files 3 1 File formats a A A a A A A EA 30 PDB files cia a A oe A a a a TA 3 1 2 X PLOR format PSF files 2 0 0 0 0 a 3 13 CHARMM19 CHARMM22 and CHARMM27 parameter files 3 4 DCD trajectory Meg simio a Ee ese ee Pe a ias ag ica 31 5 NAMD binary files maa 4 0 a amp oat eo Sek BO ee 3 2 NAMD configuration parameters 2 0 ee 32 1 Input files ete oe bed a aca ee SUR ee oa hoe ale 3222 Output files s doco 2 a he ney ee ce a ee a eee a nh ee ae 3 2 3 Standard output a2 mega ek ae ee a ee eS 3 3 AMBER force field parameters ee ee 3 4 GROMACS force field parameters 2 0 0 0 0 0202 ee eee Creating PSF Structure Files 41 Ordinary Usager cca Ok ANOLE Aa ha BR eR A BO Sh a 4 1 1 Preparing separate PDB files 2 0 0 0 0 0000
34. The total force also includes external forces Note that the loadforces command returns external forces applied by the user Therefore one can subtract the external force on an atom from the total force on this atom to get the pure force arising from the simulation system loadmasses lt varname gt Loads requested atom and group masses in amu into a local array loadmasses should only be called from within the calcforces procedure For example loadcoords m and print m 4 addforce lt atomid groupid gt lt force vector gt Applies force in kcal mol T to atom or group addforce should only be called from within the calcforces procedure For example addforce groupid 1 0 2 P addenergy lt energy kcal mol gt This command adds the specified energy to the MISC column and hence the total energy in the energy output For normal runs the command does not affect the simulation trajectory at all and only has an artificial effect on its energy output However it can indeed affect minimizations With the commands above and the functionality of the Tcl language one should be able to perform any on the fly analysis and manipulation To make it easier to perform certain tasks some Tcl routines are provided below Several vector routines vecadd vecsub vecscale from the VMD Tcl interface are defined Please refer to VMD manual for their usage The following routines take atom coordinates as input
35. Value restartFreq Description Allows to choose a different restart frequency for the collective variables 109 module Redefining it may be useful to trace the time evolution of those few properties which are not written to the trajectory file for reasons of disk space e analysis lt global Turn on run time statistical analysis gt Acceptable Values boolean Default Value off Description If this flag is enabled each colvar is instructed to perform whatever run time statistical analysis it is configured to such as correlation functions or running averages and standard deviations See section 10 2 5 for details The following is a typical configuration file The options available inside the two colvar blocks are documented in 10 2 harmonic defines an harmonic potential which is one of the available biases documented in 10 3 Note except colvar none of the keywords below is mandatory collective variables config file two distances colvarsTrajFrequency 100 output values every 100 steps colvar name ist colvar needed to identify the variable outputSystemForce yes report also the system force on this colvar in addition to the current value distance group atomNumbers 1 2 3 group2 atomNumbers 4 5 6 colvar name 2nd colvar harmonic name my_pot colvars 1st colvar 2nd colvar centers 3 0 4 0 forceConstant 5 0 In the following the section 10 2 explains how to define a colvar 10 2 2
36. a thus resulting in an appropriate overlap of the corresponding ensembles see Figure 8 Transformation between the two thermodynamic states is replaced by a series of transformations between non physical intermediate states along a well delineated pathway that connects a to b This pathway is characterized by the general extent parameter 6 35 36 44 A that makes the Hamiltonian and hence the free energy a continuous function of this parameter between a and b N AMan 5 Yo In exp 8 Mbs Pas Ait MOS Pai A 57 i 1 Here N stands for the number of intermediate stages or windows between the initial and the final states see Figure 8 11 1 3 Thermodynamic Integration An alternative to the perturbation formula for free energy calculation is Thermodynamic Integration TI With the TI method the free energy is given as 36 62 21 aa HER ay 58 In the multi configuration thermodynamic integration approach 62 implemented in NAMD OH x Px A OA the ensemble average of the derivative of the internal energy with respect to A 145 is collected for a series of discrete values and written to tiOutFile These values are analyzed by the separately distributed script NAMD_ti pl which performs the integration of individual energy components and reports back the total AA values for the transformation 11 2 Implementation of the free energy methods in NAMD The procedures implemented in NAMD are partic
37. and 2 2 2 in grid coordinates Following the comment block the maingrid and subgrids are defined in the format described above in the same order as the comment block The following parameters describe the grid based potentials e mgridforce lt apply grid forces gt Acceptable Values yes or no 87 Default Value no Description Specifies whether or not any grid forces are being applied mgridforcefile lt tag gt lt PDB file specifying force multipliers and charges for each atomd gt Acceptable Values UNIX file name Description The force on each atom is scaled by the corresponding value in this PDB file By setting the force multiplier to zero for an atom it will not be affected by the grid force mgridforcecol lt tag gt lt column of PDB from which to read force multipliers gt Acceptable Values X Y Z O or B Default Value B Description Which column in the PDB file specified by mgridforcefile contains the scaling factor mgridforcechargecol lt tag gt lt column of PDB from which to read atom charges gt Acceptable Values X Y Z O or B Default Value Atom charge used for electrostatics Description Which column in the PDB file specified by mgridforcefile contains the atom charge By default the charge value specified for the short range Columb interactions are also used for the grid force Both mgridforcecol and mgridforceqcol can be specified in which case the apparent charge of the atom wil
38. and analysis programs e g gnuplot In dimension 2 or greater integrating the discretized gradient becomes non trivial The stan dalone utility abf_integrate is provided to perform that task abf_integrate reads the gradient data and uses it to perform a Monte Carlo M C simulation in discretized collective variable space 134 specifically on the same grid used by ABF to discretize the free energy gradient By default a history dependent bias similar in spirit to metadynamics is used at each M C step the bias at the current position is incremented by a preset amount the hill height Upon convergence this bias counteracts optimally the underlying gradient it is negated to obtain the estimate of the free energy surface abf_integrate is invoked using the command line integrate lt gradient_file gt n lt nsteps gt t lt temp gt m 011 h lt hill_height gt f lt factor gt The gradient file name is provided first followed by other parameters in any order They are described below with their default value in square brackets e n number of M C steps to be performed by default a minimal number of steps is chosen based on the size of the grid and the integration runs until a convergence criterion is satisfied based on the RMSD between the target gradient and the real PMF gradient e t temperature for M C sampling unrelated to the simulation temperature 500 K e m use metadynamics like biased sampli
39. and the hydrogen borne by the Ca in glycine co exist throughout the simulation see Figure 7 yet without actually seeing each other The energy and forces are defined as a function of A in such a fashion that the interaction of the methyl group of alanine with the rest of the protein is effective at the beginning of the simulation i e A 0 while the glycine Ca hydrogen atom does not interact with the rest of the protein and vice versa at the end of the simulation i e A 1 For intermediate values of A both the alanine The features described in this section were contributed by Surjit B Dixit Christophe Chipot Nancy Universit Universit Henri Poincar France Floris Buelens Institute of Structural and Molecular Biology University of London Birkbeck UK and Christopher Harrison University of Illinois Urbana IL USA 143 A al al Na NS e o Ce H KA E Figure 7 Dual topology description for an alchemical simulation Case example of the mutation of alanine into serine The lighter color denotes the non interacting alternate state and the glycine side chains participate in nonbonded interactions with the rest of the protein scaled on the basis of the current value of A It should be clearly understood that these side chains never interact with each other It is noteworthy that end points of alchemical transformations carried out in the framework of the dual topology paradigm have been shown to be cond
40. are distinguished only by beta value This is not a normal molecular structure and may confuse other tools Arguments lt factor gt lt segid resid atomname gt segment residue or atom to be multiplied If resid is omitted the entire segment is multiplied if atomname is omitted the entire residue is multiplied May be repeated as many times as necessary to include all atoms Context After one or more segments have been built all patches applied and coordinates guessed The effects of this command may confuse other commands delatom lt segid gt resid atom name Purpose Delete one or more atoms If only segid is specified all atoms from that segment will be removed from the structure If both segid and resid are specified all atoms from just that residue will be removed If segid resid and atom name are all specified just a single atom will be removed Arguments lt segid gt Name of segment 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 definitio
41. as an atom approaches the edge of the grid 88 e mgridforcecont2 lt tag gt lt Is grid continuous in the direction of the second basis vector Acceptable Values yes or no Default Value no Description Operates the same as mgridforcecont1 except applies in the direction of the second basis vector e mgridforcecont3 lt tag gt lt Is grid continuous in the direction of the third basis vector gt Acceptable Values yes or no Default Value no Description Operates the same as mgridforcecont1 except applies in the direction of the third basis vector e mgridforcevoff lt tag gt lt Offset periodic images of the grid by specified amounts gt Acceptable Values vector of decimals x y z Default Value 000 Description If a continuous grid is used along a particular basis vector it may be desirable to shift the potentials in the image to manipulate the potential outside the grid For example consider the case where the potential is a ramp in the x direction and the grid is defined for points 0 NV with a potential f i j k given by f i j k fo i fi fo N By shifting the images of the grid the potential can be transformed as illustrated in Fig 5 e mgridforcelite lt tag gt lt Is grid to use Gridforce Lite interpolation gt Acceptable Values yes or no Default Value no Description When Gridforce Lite is enabled a faster but less accurate interpolation method is used to compute forces Specifically rat
42. cores 0 2 4 6 8 16 20 21 22 23 24 On a 4 way quad core system three cores from each socket would be 0 15 4 3 if cores on the same chip are numbered consecutively There is no need to repeat cores for each node in a run as they are reused in order For example the IBM POWER7 has four hardware threads per core and the first thread can use all of the core s resources if the other threads are idle threads 0 and 1 split the core if threads 2 and 3 are idle but if either of threads 2 or 3 are active the core is split four ways The fastest configuration of 32 threads or processes on a 128 thread 32 core is therefore setcpuaffinity pemap 0 127 4 For 64 threads we need cores 0 1 4 5 8 9 or 0 127 4 2 Running 4 processes with ppn 31 would be setcpuaffinity pemap 0 127 32 31 commap 31 127 32 For an Altix UV or other machines where the queueing system assigns cores to jobs this infor mation must be obtained with numactl show and passed to NAMD in order to set thread affinity which will improve performance namd2 setcpuaffinity numactl show awk physcpubind printf p d pemap d NF 1 2 for i 3 i lt NF 1i printf d i 17 10 CUDA GPU Acceleration Energy evaluation is slower than calculating forces alone and the loss is much greater in CUDA accelerated builds Therefore you should set outputEnergies to 100 or higher in the simulation config file Some features are unavailable in C
43. cylindrical boundary conditions gt Acceptable Values on or off Default Value off Description Specifies whether or not cylindrical boundary conditions are to be applied to the system If set to on then cylindricalBCCenter cylindricalBCr1 cylindricalBC11 and cylindricalBCk1 must be defined and cylindricalBCAxis cylindricalBCexpl cylindricalBCr2 cylindricalBC12 cylindricalBCk2 and cylindricalBCexp2 can op tionally be defined e cylindricalBCCenter lt center of cylinder A gt Acceptable Values position Description Location around which cylinder is centered e cylindricalBCAxis lt axis of cylinder A gt Acceptable Values x y or z Description Axis along which cylinder is aligned 67 cylindricalBCr1 lt radius for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect along the non axis plane of the cylinder cylindricalBC11 lt distance along cylinder axis for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect along the cylinder axis cylindricalBCk1 lt force constant for first potential gt Acceptable Values non zero decimal Description Force constant for the first harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the c
44. described in Sec 2 2 2 to run for 0 steps so that NAMD prints the pressure profile without performing any dynamics The Ewald sum method is as described in Sonne et al JCP 122 2005 The number of k vectors to use along each periodic cell dimension is specified by the pressureProfileEwaldn parameters described below pressureProfileEwaldX lt Ewald grid size along X gt Acceptable Values Positive integer Default Value 10 Description pressureProfileEwaldY lt Ewald grid size along Y gt Acceptable Values Positive integer Default Value 10 Description pressureProfileEwaldZ lt Ewald grid size along Z gt Acceptable Values Positive integer Default Value 10 Description pressureProfileAtomTypes lt Number of atom type partitions gt Acceptable Values Positive integer Default Value 1 Description If pressureProfileAtomTypes is greater than 1 NAMD will calculate the separate contributions of each type of atom to the internal bonded nonbonded and total pressure In the case of the internal contribution there will be n pressure profile data sets reported on each PPROFILEINTERNAL line where n is the number of atom types All the partial pressures for atom type 1 will be followed by those for atom type 2 and so forth The other three pressure profile reports will contain n n 1 2 data sets For example if there are n 3 atom types the six data sets arising from the three inter partition and the three intra
45. determines the target temperature of the system e loweAndersenCutoff lt cutoff radius for Lowe Andersen collisions A gt Acceptable Values positive decimal Default Value 2 7 Description Forces are only applied to atoms within this distance of one another e loweAndersenRate lt rate for Lowe Andersen collisions 1 ps gt Acceptable Values positive decimal Default Value 50 Description Determines the probability of a collision between atoms within the cutoff radius The probability is the rate specified by this keyword times the non bonded timestep 7 5 Pressure Control Constant pressure simulation and pressure calculation require periodic boundary conditions Pres sure is controlled by dynamically adjusting the size of the unit cell and rescaling all atomic coordi nates other than those of fixed atoms during the simulation Pressure values in NAMD output are in bar PRESSURE is the pressure calculated based on individual atoms while GPRESSURE incorporates hydrogen atoms into the heavier atoms to which they are bonded producing smaller fluctuations The TEMPAVG PRESSAVG and GPRESSAVG are the average of temperature and pressure values since the previous ENERGY output for the first step in the simulation they will be identical to TEMP PRESSURE and GPRESSURE The phenomenological pressure of bulk matter reflects averaging in both space and time of the sum of a large positive term the kinetic pressure nRT V and a large
46. dielectric of the solvent usually 78 5 or 80 intrinsicRadiusOffset lt shrink the intrinsic radius of atoms A gt Acceptable Values positive decimal Default Value 0 09 Description This offset shrinks the intrinsic radius of atoms used only for calculating Born radius to give better agreement with Poisson Boltzmann calculations Most users should not change this parameter ionConcentration lt concentration of ions in solvent Molar gt Acceptable Values positive decimal Default Value 0 2 Description An ion concentration of 0 M represents distilled water Increasing the ion concentration increases the electrostatic screening GBISDelta lt GB parameter for calculating Born radii gt Acceptable Values decimal Default Value 1 0 Description Use GBISDelta GBISBeta GBISGamma 1 0 0 8 4 85 for GBOPCIL and 0 8 0 0 2 90912 for GB CT See La 8 y in 50 for more information GBISBeta lt GB parameter for calculating Born radii gt Acceptable Values decimal Default Value 0 8 Description See GBISDelta GBISGamma lt GB9PC parameter for calculating Born radii gt Acceptable Values decimal Default Value 4 85 Description See GBISDelta 63 e alphaCutoff lt cutoff used in calculating Born radius and derivatives phases 1 and 3 A gt Acceptable Values positive decimal Default Value 15 Description Cutoff used for calculating Born radius Only atoms within this cutoff de sc
47. each rescaled by means of width parameters wg and we the centers of the restraint do and cg evolve with the simulation time t The joint histogram of alpha and c is also recorded on the fly o e Dual topology description for an alchemical simulation Case example of the muta tion of alanine into serine The lighter color denotes the non interacting alternate SUAUC a A eV eh A A SU eet AAA eed Convergence of an FEP calculation If the ensembles representative of states a and b are too disparate equation 56 will not converge a If in sharp contrast the configurations of state b form a subset of the ensemble of configurations characteristic of state a the simulation is expected to converge b The difficulties reflected in case a may be alleviated by the introduction of mutually overlapping intermediate states that connect a to b c It should be mentioned that in practice the kinetic contribution 7 p is assumed to be identical for state a and state b Relationship of user defined A to coupling of electrostatic or vdW interactions to a simulation given specific values of alchElecLambdaStart or alchVdwLambdaEnd Sample TI data log av against A The blue shaded area shows the integral with fine sampling close to the end point The red area shows the difference when A values are more sparse In this example insufficient sampling before A 20 1 can result in a large overestimation of the integra
48. energy output in time steps gt Acceptable Values positive integer Default Value 5 Description Every alchOutFreq number of MD steps the output file alchOutFile is updated by dumping energies that are used for ensemble averaging This variable could be set to 1 to include all the configurations for ensemble averaging Yet it is recommended to update alchOutFile energies at longer intervals to avoid large files containing highly correlated data unless a post treatment e g Bennett s acceptance ratio BAR 3 or simple overlap sampling SOS 42 is to be performed alchOutFile lt Alchemical free energy output filename gt Acceptable Values filename Default Value outfilename Description An output file named alchOutFile containing the FEP energies or tiOutFile containing the TI derivatives dumped every alchOutFreq steps alchVdwShiftCoeff lt Soft core van der Waals radius shifting coefficient gt Acceptable Values positive decimal Default Value 5 Description This is a radius shifting coefficient of A that is used to construct the modified vdW interactions during alchemical free energy calculations Providing a positive value for alchVdWShiftCoeff ensures that the vdW potential is finite everywhere for small values of A which significantly improves the accuracy and convergence of FEP and TI calculations and also prevents overlapping particles from making the simulation unstable During FEP and TI assuming A 0 den
49. 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 98 find coordinates and apply forces just like a regular atom ID Aggregate forces may then be applied to the group as whole Request remains in effect until clearconfig is called For example set groupid addgroup 14 10 12 clearconfig Clears the current list of requested atoms After clearconfig calls to addatom and addgroup can be used to build a new configuration getstep Returns the current step number loadcoords lt varname gt Loads requested atom and group coordinates in A into a local array loadcoords should only be called from within the calcforces procedure For example loadcoords p and print p 4 loadforces lt varname gt Loads the forces applied in the previous timestep in kcal mol A into a local array loadforces should only be called from within the calcforces procedure For example loadforces f and print f 4 loadtotalforces lt varname gt Loads the total forces on each requested atom in the previous time step in kcal mol A7 into a local array
50. from 0 to 1 either smoothly or in targetNumStages equally spaced discrete stages or according to an arbitrary schedule set with lambdaSchedule When the initial value of the force constant is zero an exponent greater than 1 0 distributes the effects of introducing the restraint more smoothly over time than a linear dependence and ensures that there is no singularity in the derivative of the restraint free energy with respect to lambda A value of 4 has been found to give good results in some tests targetNumSteps lt harmonic Number of steps for steering gt Acceptable Values positive integer Description Defines the number of steps required to move the restraint centers or force constant towards the values specified with targetCenters or targetForceConstant After the target values have been reached the centers resp force constant are kept fixed targetEquilSteps lt harmonic Number of steps discarded from TI estimate gt Acceptable Values positive integer Description Defines the number of steps within each stage that are considered equilibra tion and discarded from the restraint free energy derivative estimate reported reported in the output targetNumStages lt harmonic Number of stages for steering gt Acceptable Values non negative integer Default Value 0 Description If non zero sets the number of stages in which the restraint centers or force constant are changed to their target values If zero the change
51. gt Acceptable Values boolean Default Value on Description This option discretizes all hills for improved performance accumulating their energy and their gradients on two separate grids of equal spacing Grids are defined by the values of lowerBoundary upperBoundary and width for each colvar Currently this option is implemented for all types of variables except the non scalar types distanceDir or orientation If expandBoundaries is defined in one of the colvars grids are automatically expanded along the direction of that colvar e hillWidth lt metadynamics Relative width of the hills gt Acceptable Values positive decimal Default Value 27 2 Description Along each colvar the width of each Gaussian hill 2d is given by the product between this number and the colvar s width The default value gives hills whose volume is the product of W times the width of all colvars For a smoother visualization of the free energy plot decrease width and increase hillWidth in the same proportion Note when useGrids is on default in most cases values smaller than 1 should be avoided to avoid discretization errors e dumpFreeEnergyFile lt metadynamics Periodically write the PMF for visualization gt Acceptable Values boolean Default Value on Description When useGrids and this option are on the PMF is written every colvarsRestartFrequency steps to the file lt outputName gt pmf e rebinGrids lt metadynamics Recompute the g
52. in the PDB databank contain multiple chains corresponding to protein subunits water and other miscellaneous groups Protein subunits are often identified by their chain ID in the PDB file In psfgen each of these groups must be assigned to their own segment This applies most strictly in the case of protein chains each of which must be assigned to its own segment so that N terminal and C terminal patches can be applied You are free to group water molecules into whatever segments you choose Chains can be split up into their own PDB files using your favorite text editor and or Unix shell commands as illustrated in the BPTI example below If you are using VMD you can also use atom selections to write pieces of the structure to separate files Split a file containing protein and water into separate segments Creates files named myfile_water pdb myfile_frag0 pdb myfile_fragi pdb Requires VMD mol load pdb myfile pdb set water atomselect top water water writepdb myfile_water pdb set protein atomselect top protein set chains lsort unique protein get pfrag foreach chain chains set sel atomselect top pfrag chain sel writepdb myfile_frag chain 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
53. input and output file formats used by NAMD are identical to those used by CHARMM and X PLOR Input formats include coordinate files in PDB format 4 structure files in X PLOR PSF format and energy parameter files in either CHARMM or X PLOR formats Output formats include PDB coordinate files and binary DCD trajectory files These similar ities assure that the molecular dynamics trajectories from NAMD can be read by CHARMM or X PLOR and that the user can exploit the many analysis algorithms of the latter packages e Dynamics Simulation Options MD simulations may be carried out using several options including Constant energy dynamics Constant temperature dynamics via Velocity rescaling Velocity reassignment Langevin dynamics Periodic boundary conditions Constant pressure dynamics via Berendsen pressure coupling Nos Hoover Langevin piston Energy minimization Fixed atoms Rigid waters 12 Rigid bonds to hydrogen Harmonic restraints Spherical or cylindrical boundary restraints e Easy to Modify and Extend Another primary design objective for NAMD is extensibility and maintainability In order to achieve this it is designed in an object oriented style with C Since molecular dynamics is a new field new algorithms and techniques are continually being developed NAMD s modular design allows one to integrate and test new algorithms easily If you are contemplating
54. investigations underway to remove this limitation and provide full van der Waals calculations in O N time as well One of the areas of current research being studied using NAMD is the exploration of better methods for performing multiple timestep integration Currently the only available method is the impulse based Verlet 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 71 Description This parameter specifies the number of timesteps between each full elec trostatics evaluation It is recommended that fullElectFrequency be chosen so that the product of fullElectFrequency and timestep does not exceed 4 0 unless rigidBonds all or molly on is specified in which case the upper limit is perhaps doubled e nonbondedFreq lt timesteps between nonbonded evaluation gt Acceptable Values positive integer factor of fullElectFrequency Default Value
55. is calculated by the formula a COMO CINE Qi E a Olver OMe nNOS OUEEN 49 e Se oP cet cet E ie o wet AN oe Rage Te AN ee i l 43 where the score function for the Ca Ca Ca angle is defined as 2 Lael CO CO AA angf C ce err me 44 es acto Coes 0o AG and the score function for the O N 4 hydrogen bond is defined through a hBond colvar component on the same atoms The options recognized within the alpha block are e residueRange lt alpha Potential a helical residues gt Acceptable Values lt Initial residue number gt lt Final residue number gt Description This option specifies the range of residues on which this component should be defined The colvar module looks for the atoms within these residues named CA N and 0 and raises an error if any of those atoms is not found e psfSegID lt alpha PSF segment identifier gt Acceptable Values string max 4 characters Description This option sets the PSF segment identifier for the residues specified in residueRange This option need not be provided when non PSF topologies are used by NAMD 123 e hBondCoeff lt alpha Coefficient for the hydrogen bond term gt Acceptable Values positive between O and 1 Default Value 0 5 Description This number specifies the contribution to the total value from the hydrogen bond terms 0 will disable the hydrogen bond terms 1 will disable the angle
56. is continuous lambdaSchedule lt harmonic Schedule of lambda points for changing force constant gt Acceptable Values list of real numbers between 0 and 1 Description If specified together with targetForceConstant sets the sequence of discrete A values that will be used for different stages Tip A complex set of restraints can be applied to a system by defining several colvars and applying one or more harmonic restraints to different groups of colvars In some cases dozens of colvars can be defined but their value may not be relevant to limit the size of the colvars trajectory file it may be wise to disable outputValue for such ancillary variables and leave it enabled only for relevant ones 10 3 4 Multidimensional histograms The histogram feature is used to record the distribution of a set of collective variables in the form of a N dimensional histogram It functions as a collective variable bias and is invoked by adding a histogram block to the colvars configuration file 141 In addition to the common parameters name and colvars described above a histogram block may define the following parameter e outputFreq lt histogram Frequency in timesteps at which the histogram file is refreshed gt Acceptable Values positive integer Default Value Colvar module restart frequency Description The file containing histogram data is written on disk at the given time interval Like the ABF and metadyna
57. mol for energy Kelvin for temperature and bar for pressure Wallclock or CPU times are given in seconds unless otherwise noted 22 BOUNDARY energy is from spherical boundary conditions and harmonic restraints while MISC energy is from external electric fields and various steering forces TOTAL is the sum of the various potential energies and the KINETIC energy TOTAL2 uses a slightly different kinetic energy that is better conserved during equilibration in a constant energy ensemble TOTAL3 is another variation with much smaller short time fluctuations that is also adjusted to have the same running average as TOTAL2 Defects in constant energy simulations are much easier to spot in TOTAL3 than in TOTAL or TOTAL2 PRESSURE is the pressure calculated based on individual atoms while GPRESSURE incor porates hydrogen atoms into the heavier atoms to which they are bonded producing smaller fluc tuations The TEMPAVG PRESSAVG and GPRESSAVG are the average of temperature and pressure values since the previous ENERGY output for the first step in the simulation they will be identical to TEMP PRESSURE and GPRESSURE e outputEnergies lt timesteps between energy output gt 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 ever
58. 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 Briinger X PLOR Version 3 1 A System for X ray Crystallography and NMR The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry Yale University 1992 G Bussi A Laio and M Parrinello Equilibrium free energies from nonequilibrium metady namics Phys Rev Lett 96 9 090601 2006 A Carter E G Ciccotti J T Hynes and R Kapral Constrained reaction coordinate dynamics for the simulation of rare events Chem Phys Lett 156 472 477 1989 C Chipot and D A Pearlman Free energy calculations the long and winding gilded road Mol Sim 28 1 12 2002 C Chipot and A Pohorille editors Free energy calculations Theory and applications in chemistry and biology Springer Verlag 2007 G Ciccotti R Kapral and E Vanden Fijnden Blue moon sampling vectorial reaction coor dinates and unbiased constrained dynamics ChemPhysChem 6 9 1809 1814 2005 E A Coutsias C Seok and K A Dill Using quaternions to calculate RMSD J Comput Chem 25 15 1849 1857 2004 190 17 18 19 20 21 22 23 24 25 26 27 31 3
59. options are atoms refPositions or refPositionsFile refPositionsCol and refPositionsColValue In addition the following are recognized e vector lt eigenvector Vector components gt Acceptable Values space separated list of x y z triplets Description This option mutually exclusive with vectorFile sets the values of the vector components 121 e vectorFile lt eigenvector PDB file containing vector components gt Acceptable Values UNIX filename Description This option mutually exclusive with vector sets the name of a PDB file where the vector components will be read from the X Y and Z fields Note The PDB file has limited precision and fixed point numbers in some cases the vector may not be accurately represented and vector should be used instead e vectorCol lt eigenvector PDB column used to tag participating atoms gt Acceptable Values 0 or B Description Analogous to atomsCol e vectorColValue lt eigenvector Value used to tag participating atoms in the PDB file gt Acceptable Values positive decimal Description Analogous to atomsColValue This component returns a number in A whose value ranges between the smallest and largest abso lute positions in the unit cell during the simulations see also distanceZ Due to the normalization in eq 40 this range does not depend on the number of atoms involved Component gyration radius of gyration of a group of atoms The block gyration define
60. oxygen as well and read coordinates from the file to the segment SOLV Hydrogen doesn t show up in crystal structures so it is missing from this pdb file 9 Guessing missing coordinates The tolopogy file contains default internal coordinates which can be used to guess the locations of many atoms hydrogens in particular In the output pdb file the occupancy field of guessed atoms will be set to 0 atoms which are known are set to 1 and atoms which could not be guessed are set to 1 Some atoms are poorly guessed if needed bond lengths and angles were missing from the topology file Similarly waters with missing hydrogen coordinates are given a default orientation Write structure and coordinate files Now that all of the atoms and bonds have been created we can write out the psf structure file for the system We also create the matching coordinate pdb file The psf and pdb files are a matched set with identical atom ordering as needed by NAMD Using generated files in NAMD The files bpti pdb and bpti psf can now be used with NAMD but the initial coordinates require minimization first The following is an example NAMD configuration file for the BPTI example 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
61. partition interactions will be reported in the following order 1 1 1 2 1 8 2 2 2 3 3 3 The total pressure profile reported on the PRESSUREPROFILE line will contain the internal contributions in the data sets corresponding to 1 1 2 2 etc 170 e pressureProfileAtomTypesFile lt Atom type partition assignments gt Acceptable Values PDB file Default Value coordinate file Description If pressureProfileAtomTypes is greater than 1 NAMD will assign atoms to types based on the corresponding value in pressureProfileAtomTypesCol The type for each atom must be strictly less than pressureProfileAtomTypes e pressureProfileAtomTypesCol lt pressureProfileAtomTypesFile PDB column gt Acceptable Values PDB file Default Value B Description Here is an example snippet from a NAMD input that can be used to compute the Ewald component of the pressure profile It assumes that the coordinates were saved in the dcd file pp03 dcd every 500 timesteps Pme on PmeGridSizeX 64 PmeGridSizeY 64 PmeGridSizeZ 64 exclude scaled1 4 1 4scaling 1 0 switching on switchdist 9 cutoff 10 pairlistdist 11 pressureProfile on pressureProfileSlabs 30 pressureProfileFreq 100 pressureProfileAtomTypes 6 pressureProfileAtomTypesFile atomtypes pdb pressureProfileEwald on pressureProfileEwaldX 16 pressureProfileEwaldY 16 pressureProfileEwaldZ 16 set ts 0 firstTimestep ts coorfile open dcd pp03 dcd while coorfile read 1 incr
62. 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 83 e outputPairlists lt how often to print warnings gt Acceptable Values non negative integer Default Value 0 Description If an atom moves further than the pairlist tolerance during a simulation initially pairlistdist cutoff 2 but refined during the run any pairlists covering that atom are invalidated and temporary pairlists are used until the next full pairlist regeneration All interactions are calculated correctly but efficiency may be degraded Enabling outputPairlists will summarize these pairlist violation warnings periodically during the run e pairlistShrink lt tol 1 x on regeneration gt Acceptable Values non negative decimal Default Value 0 01 Description In order to maintain validity for the pairlist for an entire cycle the pairlist tolerance the distance an atom can move without causing the pairlist to be invalidated is adjusted during the simulation Every time pairlists are regenerated the tolerance is reduced by this f
63. repulsion as atoms become close 12 6 2 6 Tij Tij where rj 7 7 gives the distance between the pair of atoms The parameter Emin Urs Rmin is the minimum of the potential term Emin lt 0 which means that Emin is the well depth The Lennard Jones potential approaches 0 rapidly as rj increases so it is usually truncated smoothly shifted to 0 past a cutoff radius requiring O N computational cost The electrostatic potential is repulsive for atomic charges with the same sign and attractive for atomic charges with opposite signs Uys Emin CEQ Uelec 14 e gt 7 EOTij where ri r Fil gives the distance between the pair of atoms and q and q are the charges on the respective atoms Coulomb s constant C and the dielectric constant ey are fixed for all electrostatic interactions The parameter 14 is a unitless scaling factor whose value is 1 except for a modified 1 4 interaction where the pair of atoms is separated by a sequence of three covalent bonds so that the atoms might also be involved in a torsion angle interaction in which case 14 for a fixed constant 0 lt lt 1 Although the electrostatic potential may be computed with a cutoff like the Lennard Jones potential the 1 r potential approaches 0 much more slowly than the 1 r potential so neglecting the long range electrostatic terms can degrade qualitative results especially for highly charg
64. residue name or none Context Anywhere within segment does not affect later segments last lt patch name gt Purpose Override default patch applied to last residue in segment Default is read from topology file and may be residue specific Arguments lt patch name gt Single target patch residue name or none Context Anywhere within segment does not affect later segments residue lt resid gt lt resname gt chain Purpose Add a single residue to the end of the current segment Arguments lt resid gt Unique name for residue 1 5 characters usually numeric lt resname gt Residue type name from topology file lt chain gt Single character chain identi fier Context Anywhere within segment pdb lt file name gt Purpose Extract sequence information from PDB file when building segment Residue IDs will be preserved residue names must match entries in the topology file or should be aliased 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 A
65. separated into non overlapping constraint domains by assigning integer values in the beta column of the pdb file Forces on the atoms will be calculated for each domain independently of the other domains e TMD lt Is TMD active gt Acceptable Values on or off Default Value off Description Should TMD steering forces be applied to the system If TMD is enabled TMDk TMDFile and TMDLastStep must be defined in the input file as well e TMDk lt Elastic constant for TMD forces gt Acceptable Values Positive value in kcal mol Description The value of k in Eq 32 A value of 200 seems to work well in many cases If this setting is omitted the value in the occupancy column of the pdb file specified by TMDFile will be used as the constant for that atom This allows the user to specify the constant on a per atom basis e TMDOutputFreq lt How often to print TMD output gt Acceptable Values Positive integer Default Value 1 Description TMD output consists of lines of the form TMD ts targetRMS currentRMS where ts is the timestep targetRMS is the target RMSD at that timestep and currentRMS is the actual RMSD e TMDFile lt File for TMD information gt Acceptable Values Path to PDB file Description Target atoms are those whose occupancy O is nonzero in the TMD PDB file The file must contain the same number of atoms as the structure file The coordinates for the target structure are also taken from the targeted atoms in this
66. temperature bath Typically this would be chosen equal to or smaller than the piston period such as 100 fs 79 LangevinPistonTemp lt noise temperature K gt Acceptable Values positive decimal 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 SurfaceTensionTarget lt Surface tension target dyn cm gt Acceptable Values decimal Default Value 0 0 Description Specifies surface tension target Must be used with useFlexibleCell and periodic boundary conditions The pressure specified in LangevinPistonTarget becomes the pressure along the z axis and surface tension is applied in the x y plane StrainRate lt initial strain rate gt Acceptable Values decimal triple x y z Default Value 0 0 0 Description Optionally specifies the initial strain rate for pressure control Is overridden by value read from file specified with extendedSystem There is typically no reason to set this parameter ExcludeFromPressure lt Should some atoms be excluded from pressure rescaling gt Acceptable Values on or off Default Value off Description Specifies whether or not to exclude some atoms from pressure rescaling The coordinates and velocites of such atoms are not rescaled during constant pressure simulations though they do contribute to the virial calculation May be useful for membrane protein simulati
67. terms e angleRef lt alpha Reference Ca Ca Ca angle gt Acceptable Values positive decimal Default Value 88 Description This option sets the reference angle used in the score function 44 e angleTol lt alpha Tolerance in the Ca Ca Ca angle gt Acceptable Values positive decimal Default Value 15 Description This option sets the angle tolerance used in the score function 44 e hBondCutoff lt alpha Hydrogen bond cutoff gt Acceptable Values positive decimal Default Value 3 3 A Description Equivalent to the cutoff option in the hBond component e hBondExpNumer lt alpha Hydrogen bond numerator exponent gt Acceptable Values positive integer Default Value 6 Description Equivalent to the expNumer option in the hBond component e hBondExpDenom lt alpha Hydrogen bond denominator exponent gt Acceptable Values positive integer Default Value 8 Description Equivalent to the expDenom option in the hBond component This component returns positive values always comprised between 0 lowest a helical score and 1 highest a helical score Component dihedralPC protein dihedral pricipal component The block dihedralPC defines the parameters to calculate the projection of backbone dihedral angles within a protein segment onto a dihedral principal component following the formalism of dihedral principal component analysis dPCA proposed by Mu et al and documented in detail by A
68. 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 The value of scaled1 4 is necessary to enable the modified 1 4 VDW parameters present in the CHARMM parameter files 1 4scaling lt scaling factor for 1 4 electrostatic interactions gt Acceptable Values 0 lt decimal lt 1 Default Value 1 0 Description Scaling factor for 1 4 electrostatic interactions This factor is only used when the exclude parameter is set to scaled1 4 In this case this factor is used to modify the electrostatic interactions between 1 4 atom pairs If the exclude parameter is set to anything but scaled1 4 this parameter has no effect regardless of its value dielectric lt dielectric constant for system gt Acceptable Values decimal gt 1 0 Default Value 1 0 Description Dielectric constant for the system A value of 1
69. to make colvar components that normally calculate functions of the group s center of mass use an absolute reference position If specified disableForces is also turned on the center of mass position is x y z and zero velocities and system forces are reported e centerReference lt atom group Ignore the translations of this group gt Acceptable Values boolean Default Value off Description If this option is on the center of geometry of this group is centered on a refer ence frame determined either by refPositions or refPositionsFile This transformation occurs before any colvar component has access to the coordinates of the group hence only the recentered coordinates are available to the colvars Note the derivatives of the colvars with respect to the translation are usually neglected except by rmsd and eigenvector e rotateReference lt atom group Ignore the rotations of this group gt Acceptable Values boolean Default Value off Description If this option is on this group is rotated around its center of geometry to optimally superimpose to the positions given by refPositions or refPositionsFile This is done before recentering the group if centerReference is also defined The algorithm used is the same employed in the orientation colvar component 16 Forces applied by the colvars to this group are rotated back to the original frame prior being applied Note the derivatives of the colvars with respect to the rotation a
70. vectors of the simulation box to a coordinate frame that is centered at the center of the specified grid Note that the size and spatial coordinates of the grid remain fixed and are not scaled as the size of the simulation box fluctuates For atoms within the grid the force is computed by analytically determining the gradient of the tricubic polynomial used to interpolate the potential from surrounding grid values For atoms outside the grid the state of the mgridforcecont 1 2 3 determine whether the force is zero or computed from the images of the grid as described above Note that if the grid is ever larger than the periodic box it is truncated at the edge of that box The consequence of this is that the computed potential will not vary smoothly at the edges introducing numerical instability NAMD also supports non uniform grids allowing regions of a grid to be defined at higher resolution Non uniform grids are structured hierarchically with a single maingrid which has one or more subgrids Each subgrid spans a number of maingrid cells in each of the three dimensions and effectively redefines the data in that region The subgrids are usually defined at higher resolution with the restriction that the number of cells along each dimension is an integral number of the original number in the maingrid Note that the maingrid still has data points in regions where subgrids are defined and that on the boundary of a subgrid they must agree with the va
71. zero net force or torque to the system is generated which may lead to undesired trans lations or rotations of the system Note to minimize the length of the NAMD standard output messages in the atom group s con figuration are not echoed by default This can be overcome by the boolean keyword verboseOutput within the group Recommendations for using atom groups When defining the atom groups for a collective variable these guidelines should be followed to avoid inconsistencies and performance losses e In simulations with periodic boundary conditions NAMD maintains the coordinates of all the atoms within a molecule contiguous to each other i e there are no spurious jumps in the molecular bonds The colvar module relies on this when calculating a group s center of mass but this condition may fail when the group spans different molecules in that case writing the NAMD output files wrapA11 or wrapWater could produce wrong results when a simulation run is continued from a previous one There are however cases in which wrapA11 or wrapWater can be safely applied i the group has only one atom ii it has all its atoms within the same molecule iii it is used by a colvar component which does not access its center of mass and uses instead only interatomic distances coordNum hBond alpha 128 iv it is used by a colvar component that ignores the ill defined Cartesian components of its center of mass such as the x and y compon
72. 000 0100 0010 0001 with different matrices separated by a single blank line and no line before the first or after the last matrix This file is OPTIONAL Leave this line out to have namd generate the transformations for you e symmetryFirstStep lt first symmetry restraint timestep gt Acceptable Values Non negative integer Default Value 0 Description e symmetryLastStep lt last symmetry restraint timestep gt Acceptable Values Positive integer Default Value infinity Description Symmetry restraints are applied only between symmetryFirstStep and symmetryLastStep Use these settings with caution and ensure restraints are only being applied when necessary e g not during equilibration 9 7 Targeted Molecular Dynamics TMD In TMD subset of atoms in the simulation is guided towards a final target structure by means of steering forces At each timestep the RMS distance between the current coordinates and the 93 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 RM S t RMS t 31 where RMS t is the instantaneous best fit RMS distance of the current coordinates from the target coordinates and RM S t evolves linearly from the initial RMSD at the first TMD step to the final RMSD at the last TMD step The spring constant k is scaled down by the number N of targeted atoms Atoms can be
73. 0002 ae 4 1 2 Deleting unwanted atoms 1 e 4 2 BRTLEXample ea koa Se Ea leg ek Ge D oe we ae A 4 3 Building solvent around a protein soa oa a 4 4 List of Commands aaa 4 5 Example of a Session Log ee Force Field Parameters 5 1 Potential energy functions 2 2 5 1 1 Bonded potential energy terms 0 020000 ee ee eee 5 1 2 Nonbonded potential energy terms e o 5 2 Non bonded interactions a 5 2 1 Van der Waals interactions e 5 2 2 Electrostatic interactions e 5 2 3 Non bonded force field parameters o e 5 2 4 PME parameters io ici Be Re Soh A o Ha 5 2 5 Full direct parameters 2 a 5 2 6 Tabulated nonbonded interaction parameters o 11 11 13 14 14 14 14 15 17 18 18 18 18 18 18 19 19 19 20 22 24 26 28 28 29 29 30 34 35 40 Bio Water Models 10 ii of Ao ne os eR EE es et te Ce A 5 4 Drude polarizable force field 2 2 0 00 pee ee 5 4 1 Required input files e 5 4 2 Standard output 22 30 80404 2 dee Re ee ee a ae a 5 4 3 Drude force field parameters o 5 5 MARTINI Residue Based Coarse Grain Forcefield o o 5 6 Constraints and Restraints a a 5 6 1 Bond constraint parameters e 5 6 2 Harmonic restraint parameters e 5 6 3 Fixed atoms parameters 5 6 4 Extra bond ang
74. 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 verletI is the same as r RESPA constant naive is the stale force extrapolation method e longSplitting lt how should long and short range forces be split gt Acceptable Values c1 c2 Default Value c1 Description Specifies the method used to split electrostatic forces between long and short range potentials The c1 option uses a cubic polynomial splitting function 3 r 1 r 3 Sa r 2 2 to affect C continuity in the splitting of the electrostatic potential 59 The c2 option uses a quintic polynomial splitting function ma 3 ae 4 r 5 so Y to affect C continuity in the splitting of the electrostatic potential The S splitting func tion contributed by Bruce Berne Ruhong Zhou and Joe Morrone produces demonstrably better long time stability than S3 without requiring any additional computational cost during simulation since the nonbonded forces are c
75. 10 1 2 Output files By default the collective variables module writes three output files e a state file named lt outputName gt colvars state this file is in ASCII format regardless of the value of binaryOutput in the NAMD configuration the name of this file can be provided as colvarsInput to continue the simulation in the next run e a restart file equivalent to the state file is written every colvarsRestartFrequency steps if either colvarsRestartFrequency or the NAMD parameter restartFreq is defined its name is lt restartName gt colvars state and can be given as colvarsInput to continue an interrupted run provided that the coordinates and velocities restart files at the same time step are also used e a trajectory file is written during the simulation if the colvars module pa rameter colvarsTrajFrequency is greater than 0 default 100 its name is lt outputName gt colvars traj unlike the state file it is not needed to restart a simulation but can be read in for post processing see 10 2 5 Other output files may be written by specific methods applied to the colvars e g by the ABF method see 10 3 1 or the metadynamics method see 10 3 2 Like the colvar trajectory file they are needed only for analyzing not continuing a simulation All such files names also begin with the prefix lt outputName gt 10 1 3 Colvars module configuration file Except for the three NAMD keywords listed above colvars colvarsConfig
76. 10 2 4 Defining atom STOUDS ates aa Set She ds ee ee ol ie 10 2 5 Statistical analysis of individual collective variables 10 3 Biasing and analysis methods aoaaa ee 10 3 1 Adaptive Biasing Force e 10 3 2 Metadynamics 10 3 3 Harmonic restraints and Steered Molecular Dynamics 10 3 4 Multidimensional histograms 0 0 0000 eee eee 11 Alchemical Free Energy Methods 11 1 Theoretical Background 2 ee 11 1 1 The dual topology paradigm 0 000000 eee ee 11 1 2 Free Energy Perturbation 0 0 000002 eee eee 11 1 3 Thermodynamic Integration 0 0 000002 eee ee 11 2 Implementation of the free energy methods in NAMD 11 3 Examples of input files for running alchemical free energy calculations 11 4 Description of a free energy calculation output 2 e 11 4 1 Free Energy Perturbation 0 0 002 2p eee ee ee 11 4 2 Thermodynamic Integration 2 2 0 o 12 Accelerated Sampling Methods 12 1 Accelerated Molecular Dynamics 00000 eee ee 12 1 1 Theoretical background e 12 12 NAMD parameters cues SO gS A eee PO eg 12 2 Adaptive Tempering 85 85 85 86 89 90 92 93 95 97 98 101 104 106 106 106 108 108 111 111 114 125 125 129 130 131 135 139 141 143 143 143 144 145 146 149 151 151 151 12 21 NAMD parameters s a a Poe ee Ue ee oe AS
77. 14 2399 2407 1998 W F van Gunsteren Methods for calculation of free energies and binding constants Successes and problems In W F Van Gunsteren and P K Weiner editors Computer simulation of biomolecular systems Theoretical and experimental applications pages 27 59 Escom The Netherlands 1989 A F Voter Hyperdynamics Accelerated molecular dynamics of infrequent events Phys Rev Lett 78 20 3908 3911 May 1997 Y Wang C Harrison K Schulten and J McCammon Implementation of accelerated molec ular dynamics in NAMD Comp Sci Discov 4 015002 2011 J Weiser P Senkin and W C Still Approximate atomic surfaces from linear combinations of pairwise overlaps LCPO J Comp Chem 20 217 230 1999 R W Zwanzig High temperature equation of state by a perturbation method i nonpolar gases J Chem Phys 22 1420 1426 1954 194 Index 1 4scaling parameter 46 abort command 16 accelMD parameter 154 accelMDalpha parameter 154 accelMDdihe parameter 154 accelMDdual parameter 154 accelMDE parameter 154 accelMDFirstStep parameter 155 accelMDLastStep parameter 155 accelMDOutFreq parameter 155 accelMDTalpha parameter 155 accelMDTE parameter 155 adaptTempBins parameter 156 adaptTempCgamma parameter 157 adaptTempDt parameter 156 adaptTempFirstStep parameter 157 adaptTempFreq parameter 156 adaptTempInFile parameter 156 adaptTempLangevin parameter 157 adaptTempLastStep parameter
78. 157 adaptTempMD parameter 156 adaptTempOutFreq parameter 157 adaptTempRandom parameter 157 adaptTempRescaling parameter 157 adaptTempRestartFile parameter 157 adaptTempRestartFreq parameter 157 adaptTempTmax parameter 156 adaptTempTmin parameter 156 alch parameter 146 alchCol parameter 147 alchDecouple parameter 149 alchElecLambdaStart parameter 147 alchEquilSteps parameter 146 alchFile parameter 146 alchLambda parameter 16 146 alchLambda2 parameter 16 146 alchOutFile parameter 147 alchOutFreq parameter 147 alchType parameter 146 alchVdwLambdaEnd parameter 148 alchVdwShiftCoeff parameter 147 alias psfgen command 35 39 alphaCutoff parameter 64 195 amber parameter 24 ambercoor parameter 24 analysis parameter 110 angleRef parameter 124 angleTol parameter 124 applyBias parameter 134 atomNameResidueRange parameter 126 atomNumbers parameter 126 atomNumbersRange parameter 126 Atoms moving too fast 82 atoms parameter 120 atomsCol parameter 126 atomsColValue parameter 127 atomsFile parameter 126 auto psfgen command 36 axis parameter 117 Bad global exclusion count 82 BerendsenPressure parameter 15 77 BerendsenPressureCompressibility parame ter 15 78 BerendsenPressureFreq parameter 78 BerendsenPressureRelaxationTime ter 15 78 BerendsenPressureTarget parameter 15 78 binaryoutput parameter 21 binaryrestart parameter 21 bincoordinates parameter 20 binvelo
79. 2 Component distanceDir distance unit vector between two groups The distanceDir block defines a distance unit vector component which accepts the same key words as distance group1 group2 and forceNoPBC It returns a 3 dimensional unit vector d dy dy dz with d 1 Component angle angle between three groups The angle block defines an angle and contains the three blocks group1 group2 and group3 defining the three groups It returns an angle in degrees within the interval 0 180 Component dihedral torsional angle between four groups The dihedral block defines a torsional angle and contains the blocks group1 group2 group3 and group4 defining the four groups It returns an angle in degrees within the interval 180 180 The colvar module calculates all the distances between two angles taking into account periodicity For instance reference values for restraints or range boundaries can be defined by using any real number of choice 118 e oneSiteSystemForce lt angle dihedral Measure system force on group 1 only gt Acceptable Values boolean Default Value no Description If this is set to yes the system force is measured along a vector field see equation 50 in section 10 3 1 that only involves atoms of group1 See section 10 3 1 for an example Component coordNum coordination number between two groups The coordNum block defines a coordination number or number of contacts
80. 2 E Darve and A Pohorille Calculating free energies using average force J Chem Phys 115 20 9169 9183 NOV 22 2001 E Darve D Rodr guez G mez and A Pohorille Adaptive biasing force method for scalar and vector free energy calculations J Chem Phys 128 14 144120 2008 W K den Otter Thermodynamic integration of the free energy along a reaction coordinate in cartesian coordinates J Chem Phys 112 7283 7292 2000 Y Deng and B Roux Computations of standard binding free energies with molecular dynamics simulations J Phys Chem B 113 8 2234 2246 2009 D Frenkel and B Smit Understanding Molecular Simulation From Algorithms to Applications Academic Press California 2002 J Gao K Kuczera B Tidor and M Karplus Hidden thermodynamics of mutant proteins A molecular dynamics analysis Science 244 1069 1072 1989 M K Gilson J A Given B L Bush and J A McCammon The statistical thermodynamic basis for computation of binding affinities A critical review Biophys J 72 1047 1069 1997 H Grubmiiller Predicting slow structural transitions in macromolecular systems Conforma tional flooding Phys Rev E 52 3 2893 2906 Sep 1995 D Hamelberg C de Oliveira and J McCammon Sampling of slow diffusive conformational transitions with accelerated molecular dynamics J Chem Phys 127 155102 2007 D Hamelberg J Mongan and J McCammon Accelerated molecular dynamics a promising
81. 4 3 055469e 17 0 02 7 956951e 12 2 387085e 15 0 03 6 985526e 11 1 397105e 14 13 98 0 000000e 00 0 000000e 00 13 99 0 000000e 00 0 000000e 00 TYPE 00 O 1 832907e 27 1 099744e 32 0 01 1 832907e 15 1 099744e 18 0 02 2 863917e 13 8 591751e 15 0 03 2 514276e 12 5 028551e 14 13 98 0 000000e 00 0 000000e 00 13 99 0 000000e 00 0 000000e 00 TYPE SISI O 0 000000e 00 0 000000e 00 0 01 0 000000e 00 0 000000e 00 13 98 0 000000e 00 0 000000e 00 13 99 0 000000e 00 0 000000e 00 The following three parameters are required for tabulated energies e tabulatedEnergies lt use tabulated energies gt Acceptable Values yes or no Default Value no Description Specifies whether or not tabulated energies will be used for van der Waals interactions between specified pairs of atom types e tabulatedEnergiesFile lt file containing energy table gt Acceptable Values file name Description Provides one energy table for each interaction type in parameter file See format above e tableInterpType lt cubic or linear interpolation gt Acceptable Values cubic or linear Description Specifies the order for interpolating between energy table entries 50 5 3 Water Models NAMD currently supports the 3 site TIP3P water model the 4 site TIP4P water model and the 5 site SWM4 NDP water model from the Drude force field 40 TIP3P is the current default water model Usage of alternative water models is described below e waterModel lt
82. D Bashford and D A Case Modification of the generalised born model suitable for macromolecules J Phys Chem 104 3712 3720 2000 A Onufriev D Bashford and D A Case Exploring protein native states and large scale conformational changes with a modified generalized born model Proteins Struct Func Gen 55 383 394 2004 D A Pearlman A comparison of alternative approaches to free energy calculations J Phys Chem 98 1487 1493 1994 P Raiteri A Laio F L Gervasio C Micheletti and M Parrinello Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics J Phys Chem B 110 8 3533 9 2005 A Roitberg and R Elber Modeling side chains in peptides and proteins Application of the locally enhanced sampling technique and the simulated annealing methods to find minimum energy conformations J Chem Phys 95 9277 9287 1991 M J Ruiz Montero D Frenkel and J J Brey Efficient schemes to compute diffusive barrier crossing rates Mol Phys 90 925 941 1997 M Schaefer and C Froemmel A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution J Mol Biol 216 1045 1066 1990 M R Shirts D L Mobley J D Chodera and V S Pande Accurate and efficient corrections for missing dispersion interactions in molecular simulations The Journal of Physical Chemistry B 111 45 13052 13063 2007 C Simmerling T Fox a
83. D binary files are stored in NAMD internal units and must be multiplied by PDBVELFACTOR 20 45482706 to convert to A ps Forces in NAMD binary files are stored in kcal mol A 3 2 NAMD configuration parameters 3 2 1 Input files e coordinates lt coordinate PDB file gt Acceptable Values UNIX filename Description The PDB file containing initial position coordinate data Note that path names can be either absolute or relative Only one value may be specified e structure lt PSF file gt Acceptable Values UNIX filename Description The X PLOR format PSF file describing the molecular system to be simu lated Only one value may be specified e parameters lt parameter file gt Acceptable Values UNIX filename Description A CHARMM19 CHARMM22 or CHARMM27 parameter file that defines all or part of the parameters necessary for the molecular system to be simulated At least one parameter file must be specified for each simulation Multiple definitions but only one file per definition are allowed for systems that require more than one parameter file The files will be read in the order that they appear in the configuration file If duplicate parameters are read a 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 D
84. D supports a maximum of 255 copies which should be sufficient Begin by generating the complete molecular structure and guessing coordinates as described in Sec 4 As the last operation in your script prior to writing the psf and pdb files add the multiply command specifying the number of copies desired and listing segments residues or atoms to be multiplied For example multiply 4 BPTI 56 BPTI 57 will create four copies of the last two residues of segment BPTI You must include all atoms to be enhanced in a single multiply command in order for the bonded terms in the psf file to be duplicated 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 O for normal atoms and varies from 1 to the number of copies created for enhanced atoms The enhanced atoms may be easily observed in VMD with the atom selection beta 0 12 3 2 Simulation In practice LES is a simple method used to increase sampling no special output is generated The following parameters are used to enable LES e les lt is locally enhanced sampling active gt Acceptable Values on or off Default Value off Description Specifies whether or not LES is active lesFactor lt
85. Data Bank at http www pdb org by searching for 6PTI and downloading the complete structure file in PDB format Building the BPTI structure In this demo we create the files bpti psf and bpti pdb in the output directory which can then be used for a simple NAMD simulation File bpti_example tcl Requirements topology file top_al122_prot inp in directory toppar PDB file 6PTI pdb in current directory Create working directory remove old output files mkdir p output rm f output 6PTI_protein pdb output 6PTI_water pdb 1 Split input PDB file into segments grep v HETATM 6PTI pdb gt output 6PTI_protein pdb grep HOH 6PTI pdb gt output 6PTI_water pdb 2 Embed the psfgen commands in this script psfgen lt lt ENDMOL 3 Read topology file topology toppar top_al122_prot inp 4 Build protein segment segment BPTI 30 pdb output 6PTI_protein pdb 5 Patch 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 coo
86. E the Ewald contribution should be estimated using a separate offline calculation based on the saved trajectory files The nonbonded contribution using a cutoff different from the one used in the simulation may also be computed offline in the same fashion as for Ewald if desired Pressure profile calculations may be performed in either constant volume or constant pressure conditions If constant pressure is enabled the slabs thickness will be rescaled along with the unit cell the dcdUnitCell option will also be switched on so that unit cell information is stored in the trajectory file NAMD 2 6 now reports the lateral pressure partitioned by interaction type Three groups are reported kinetic rigid bond restraints referred to as internal bonded and nonbonded If Ewald pressure profile calculations are active the Ewald contribution is reported in the nonbonded section and no other contributions are reported NAMD 2 6 also permits the pressure profile to be partitioned by atom type Up to 15 atom groups may be assigned and individual contribution of each group for the internal pressures and the pairwise contributions of interactions within and between groups for the nonbonded and bonded pressures are reported in the output file e pressureProfile lt compute pressure profile gt Acceptable Values on or off Default Value off Description When active NAMD will compute kinetic bonded and nonbonded but not reciprocal spac
87. EX_EVENTS 100000 NPROC PBS_NNODES 6 aprun n NPROC N 2 d 6 namd2 ppn 5 setcpuaffinity pemap 1 8 10 11 commap 0 9 For three processes per node use setenv MPICH_PTL_UNEX_EVENTS 100000 NPROC PBS_NNODES 4 aprun n NPROC N 3 d 4 namd2 ppn 3 setcpuaffinity pemap 1 5 7 8 10 11 commap 0 6 9 The strange pemap and commap settings place the communication threads on cores that have been observed to have higher operating system loads 17 7 SGI Altix UV Use Linux x86_64 multicore and the following script to set CPU affinity namd2 setcpuaffinity numactl show awk physcpubind printf p d pemap d NF 1 2 for i 3 i lt NF i printf d i For runs on large numbers of cores you will need to experiment use the following to enable the Charm communication thread namd2 setcpuaffinity numactl show awk physcpubind printf p d pemap d NF 2 2 for i 3 i lt NF i printf d i print commthread commap NF 183 17 8 IBM POWER Clusters Run the MPI version of NAMD as you would any POE program The options and environment variables for poe are various and arcane so you should consult your local documentation for rec ommended settings As an example to run on Blue Horizon one would specify poe namd2 lt configfile gt nodes lt procs 8 gt tasks_per_node 8 17 9 CPU Affinity NAMD may run faster on some machines if threa
88. Go model in NAMD introduces the idea of chain types Consider modeling a protein nucleic acid complex Using classical all atom MD a single force field describes all possible nonbonded interactions With Go however one can create separate nonbonded force fields to describe the protein and nucleic acid interactions In order to create separate force fields atoms are grouped together using chain types where the chain types are taken from the occupancy field of the reference PDB file For argument sake assume that the protein atoms have an occupancy value of 1 0 and that the nucleic acid atoms have an occupancy value of 2 0 One now must define three separate Go potentials for intra protein intra nucleic acid and inter protein nucleic acid interactions In terms of chain types this corresponds to 1 between atom pairs fully in chain 1 2 between atom pairs fully in chain 2 3 between atom pairs where one atom is in chain 1 and the other atom is in chain 2 respectively To run Go a minimum of one chain type must be defined 13 3 Configuration file modifications The following configuration parameters are used to setup and run a Go simulation e GoForcesOn lt Are Go forces turned on gt Acceptable Values on or off Default Value off Description Specifies whether or not Go forces should be calculated If turned off Go forces will not be calculated If turned on Go forces will be calculated By default the Go forces will be
89. MD formats e gromacs lt use GROMACS format force field gt Acceptable Values on or off Default Value off Description If gromacs is set to on then grotopfile must be defined and structure and parameters should not be defined e grotopfile lt GROMACS format topology parameter file gt Acceptable Values UNIX filename Description This file contains complete topology and parameter information of the system e grocoorfile lt GROMACS format coordinate file gt Acceptable Values UNIX filename Description This file contains the coordinates of all the atoms Note that coordinates 26 can also be used for PDB format coordinate file When gromacs is set to on either grocoorfile or coordinates must be defined but not both However NAMD does not have support for many GROMACS specific options e Dummies fake atoms with positions generated from the positions of real atoms are not supported e The GROMACS pairs section where explicit 1 4 parameters are given between pairs of atoms is not supported since NAMD calculates its 1 4 interactions exclusively by type e Similarly exclusions are not supported The biggest problem here is that 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 wil
90. 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 atoms in gro
91. RAMD simulations in which the randomly oriented acceleration is applied continuously and ii combined RAMD MD simulations in which RAMD steps alternate with standard MD steps Additional information is found in the README file in the lib ramd directory The user is encouraged to carefully read this information before starting production runs The three required scripts are stored in lib ramd scripts i ramd 4 0 tcl defines the sim ulation parameters and passes them from the NAMD configuration file to the main script ii ramd 4 0_script tcl adds the randomly oriented force and performs all related computations and iii vectors tcl was borrowed from VMD and defines the vector operations used Two examples for running the scripts are included in the directory lib ramd examples The user is encouraged to read the 7 README examples file provided in the same directory In order to turn RAMD on the line source path to your files ramd 4 0 tc1 should be in cluded in the NAMD configuration file Unless the user decides to store the scripts at a different location the path path to your files should point to the lib ramd scripts directory Other wise the user should make sure that the directory path to your files stores all three scripts described above The specific RAMD simulation parameters to be provided in the NAMD configuration file listed below should be preceded by the keywo
92. Restarting the simulation will 81 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 also regenerate the patch grid In rare special circumstances atoms that are involved in bonded terms bonds angles dihedrals or impropers or nonbonded exclusions especially implicit exclusions due to bonds will be placed on non neighboring patches because they are more than the cutoff distance apart This can result in the simulation dying with a message of bad global exclusion count If an atoms moving too fast simulation has become unstable bad global exclusion count or similar error happens on the first timestep then there is likely something very wrong with the input coordinates such as the atoms with uninitialized coordinates or different atom orders in the PSF and PDB file Looking at the system in VMD will often reveal an abnormal structure Be aware that the atom IDs in the Atoms moving too fast error message are 1 based while VMD s atom indices are 0 based If an atoms moving too fast simulation has become unstable bad global exclusion count or similar error happens later in the simulation then the dynamics have pr
93. Script parameter 98 tCouple parameter 74 tCoupleCol parameter 74 tCoupleFile parameter 74 tCoupleTemp parameter 74 TEMPAVG 23 temperature parameter 70 timestep parameter 70 MD parameter 94 MDDiffRMSD parameter 95 MDFile parameter 94 MDFile2 parameter 95 MDFinalRMSD parameter 95 MDFirstStep parameter 94 MDInitialRMSD parameter 95 MDk parameter 94 MDLastStep parameter 94 MDOutputFreq parameter 94 topology psfgen command 35 TOTAL2 energy 23 T T T T T T T T T T 200 TOTALS energy 23 twoAwayX 187 twoAway Y 187 twoAwayZ 187 units used for output 18 19 22 updateBias parameter 134 upperBoundary parameter 112 upperWall parameter 112 upperWallConstant parameter 112 useConstantArea parameter 15 77 useConstantRatio parameter 15 77 useFlexibleCell parameter 15 77 useGrids parameter 137 useGroupPressure parameter 15 77 useSettle parameter 55 vdwForceSwitching parameter 45 vdwGeometricSigma parameter 46 vector parameter 121 vectorCol parameter 122 vectorColValue parameter 122 vectorFile parameter 122 125 vectorNumber parameter 125 velDCDfile parameter 22 velDCDfreq parameter 22 velocities parameter 20 velocityQuenching parameter 69 waterModel parameter 51 width parameter 111 wrapAll parameter 66 wrapAround parameter 115 wrapNearest parameter 66 wrapWater parameter 66 writeHillsTrajectory parameter 139 writepdb psfgen command 40 writepsf psfgen comm
94. U r y Ubonded F y Unonbonded 7 2 over a large number of bonded and nonbonded terms The bonded potential terms involve 2 3 and 4 body interactions of covalently bonded atoms with O N terms in the summation The nonbonded potential terms involve interactions between all pairs of atoms usually excluding pairs of atoms already involved in a bonded term with O N terms in the summation although fast evaluation techniques are used to compute good approximations to their contribution to the potential with O N or O N log N computational cost 5 1 1 Bonded potential energy terms The bonded potential terms involve 2 3 and 4 body interactions of covalently bonded atoms The 2 body spring bond potential describes the harmonic vibrational motion between an i 7 pair of covalently bonded atoms Ubond k rij ro 3 where rj 17 m gives the distance between the atoms ro is the equilibrium distance and k is the spring constant The 3 body angular bond potential describes the angular vibrational motion occurring between an i j k triple of covalently bonded atoms Uangle ko 0 a 6 F kub Tik Tub 4 where in the first term 0 is the angle in radians between vectors fij rj T and fki Tj Tk Oo is the equilibrium angle and kg is the angle constant The second term is the Urey Bradley term used to describe a noncovalent spring between the outer i and k atoms active when const
95. UDA builds including alchemical free energy perturbation and the Lowe Andersen thermostat 184 As this is a new feature you are encouraged to test all simulations before beginning production runs Forces evaluated on the GPU differ slightly from a CPU only calculation an effect more visible in reported scalar pressure values than in energies To benefit from GPU acceleration you will need a CUDA build of NAMD and a recent high end NVIDIA video card CUDA builds will not function without a CUDA capable GPU You will also need to be running the NVIDIA Linux driver version 270 41 19 or newer released Linux binaries are built with CUDA 4 0 but can be built with newer versions as well Finally the libcudart so 4 included with the binary the one copied from the version of CUDA it was built with must be in a directory in your LD_LIBRARY_PATH before any other libcudart so libraries For example when running a multicore binary recommended for a single machine setenv LD_LIBRARY_PATH LD_LIBRARY_PATH or LD_LIBRARY_PATH LD_LIBRARY_PATH export LD_LIBRARY_PATH namd2 idlepoll p4 lt configfile gt When running CUDA NAMD always add idlepoll to the command line This is needed to poll the GPU for results rather than sleeping while idle Each namd2 thread can use only one GPU Therefore you will need to run at least one thread for each GPU you want to use Multiple threads can share a single GPU usually with an increase in performanc
96. a particular modification to NAMD you are encouraged to contact the developers for guidance e Interactive MD simulations A system undergoing simulation in NAMD may be viewed and altered with VMD for instance forces can be applied to a set of atoms to alter or rearrange part of the molecular structure For more information on VMD see http www ks uiuc edu Research vmd e Load Balancing An important factor in parallel applications is the equal distribution of computational load among the processors In parallel molecular simulation a spatial decomposition that evenly distributes the computational load causes the region of space mapped to each processor to become very irregular hard to compute and difficult to generalize to the evaluation of many different types of forces NAMD addresses this problem by using a simple uniform spatial decomposition where the entire model is split into uniform cubes of space called patches An initial load balancer assigns patches and the calculation of interactions among the atoms within them to processors such that the computational load is balanced as much as possible During the simulation an incremental load balancer monitors the load and performs necessary adjustments 1 2 Acknowledgments 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 Theoretic
97. ability of system forces is necessary The following colvar components can be used in ABF calculations distance distance_xy distance_z angle dihedral gyration rmsd and eigenvector Atom groups may not be replaced by dummy atoms unless they are excluded from the force measurement by specifying oneSiteSystemForce if available 3 Mutual orthogonality of colvars In a multidimensional ABF calculation equation 48 must be satisfied for any two colvars and Various cases fulfill this orthogonality condition e and are based on non overlapping sets of atoms e atoms involved in the force measurement on do not participate in the definition of This can be obtained using the option oneSiteSystemForce of the distance angle and dihedral components example Ramachandran angles 4 e and are orthogonal by construction Useful cases are the sum and difference of two components or distance_z and distance_xy using the same axis 4 Mutual orthogonality of components when several components are combined into a colvar it is assumed that their vectors v equation 50 are mutually orthogonal The cases described for colvars in the previous paragraph apply 5 Orthogonality of colvars and constraints equation 49 can be satisfied in two simple ways if either no constrained atoms are involved in the force measurement see point 3 above or pairs of atoms joined by a constraint bond are part of an atom gro
98. aining force constant gt Acceptable Values X Y Z 0 or B Description Column of the PDB file to use for the harmonic constraint force constant This parameter may specify any of the floating point fields of the PDB file either X Y Z occupancy or beta coupling temperature coupling Regardless of which column is used a value of 0 indicates that the atom should not be constrained Otherwise the value specified is used as the force constant for that atom s restraining potential 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 55 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 coordi
99. al Biophysics Group past and present who have helped tremendously in making suggestions pushing for new features and testing bug ridden code 13 2 Getting Started 2 1 What is needed Before running NAMD explained in section 17 the following are be needed e A CHARMM force field in either CHARMM or X PLOR format e An X PLOR format PSF file describing the molecular structure e The initial coordinates of the molecular system in the form of a PDB file e A NAMD configuration file NAMD provides the psfgen utility documented in Section 4 which is capable of generating the required PSF and PDB files by merging PDB files and guessing coordinates for missing atoms If psfgen is insufficient for your system we recommend that you obtain access to either CHARMM or X PLOR both of which are capable of generating the required files 2 2 NAMD configuration file Besides these input and output files NAMD also uses a file referred to as the configuration file This file specifies what dynamics options and values that NAMD should use such as the number of timesteps to perform initial temperature etc The options and values in this file control how the system will be simulated A NAMD configuration file contains a set of options and values The options and values specified determine the exact behavior of NAMD what features are active or inactive how long the simulation should continue etc Section 2 2 1 describes how options are specified with
100. al interaction terms consisting of bonded interactions between 2 3 and 4 atoms and pairwise interactions including electrostatic and van der Waals forces This commonality allows simulations to migrate between these three programs e Efficient Full Electrostatics Algorithms NAMD incorporates the Particle Mesh Ewald PME algorithm which takes the full elec trostatic interactions into account This algorithm reduces the computational complexity of electrostatic force evaluation from O N to O N log N e Multiple Time Stepping The velocity Verlet integration 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
101. alculated via a lookup table Note that earlier options xplor and sharp are no longer supported e molly lt use mollified impulse method MOLLY gt Acceptable Values on or off Default Value off Description This method eliminates the components of the long range electrostatic forces which contribute to resonance along bonds to hydrogen atoms allowing a fullElectFrequency of 6 vs 4 with a 1 fs timestep without using rigidBonds all You may use rigidBonds water but using rigidBonds all with MOLLY makes no sense since the degrees of freedom which MOLLY protects from resonance are already frozen 72 e mollyTolerance lt allowable error for MOLLY gt Acceptable Values positive decimal Default Value 0 00001 Description Convergence criterion for MOLLY algorithm e mollyIterations lt maximum MOLLY iterations gt Acceptable Values positive integer Default Value 100 Description Maximum number of iterations for MOLLY algorithm 7 4 Temperature Control and Equilibration 7 4 1 Langevin dynamics parameters NAMD is capable of performing Langevin dynamics where additional damping and random forces are introduced to the system This capability is based on that implemented in X PLOR which is detailed in the X PLOR User s Manual 10 although a different integrator is used e langevin lt use Langevin dynamics gt Acceptable Values on or off Default Value off Description Specifies whether or not Langevin dynamics activ
102. allel to a unit cell vector The following keywords can be used within periodic components and are illegal elsewhere e period lt distanceZ Period of the component gt Acceptable Values positive decimal Default Value 0 0 Description Setting this number enables the treatment of distanceZ as a periodic com ponent by default distanceZ is not considered periodic The keyword is supported but irrelevant within dihedral or spinAngle because their period is always 360 degrees e wrapAround lt distanceZ dihedral or spinAngle Center of the wrapping interval for periodic variables gt Acceptable Values decimal Default Value 0 0 Description By default values of the periodic components are centered around zero ranging from P 2 to P 2 where P is the period Setting this number centers the interval around this value This can be useful for convenience of output or to set lowerWall and upperWall in an order that would not otherwise be allowed Internally all differences between two values of a periodic colvar follow the minimum image con vention they are calculated based on the two periodic images that are closest to each other Note linear or polynomial combinations of periodic components may become meaningless when components cross the periodic boundary Use such combinations carefully estimate the range of possible values of each component in a given simulation and make use of wrapAround to limit this problem whenever possi
103. alue no Description Turns on particle mesh Ewald e PMETolerance lt PME direct space tolerance gt Acceptable Values positive decimal Default Value 107 Description Affects the value of the Ewald coefficient and the overall accuracy of the results e PMEInterpOrder lt PME interpolation order gt Acceptable Values positive integer 47 Default Value 4 cubic Description Charges are interpolated onto the grid and forces are interpolated off using this many points equal to the order of the interpolation function plus one PMEGridSpacing lt maximum space between grid points gt Acceptable Values positive real Description The grid spacing partially determines the accuracy and efficiency of PME If any of the grid sizes below are not set then PMEGridSpacing must be set recommended value is 1 0 A and will be used to calculate them If a grid size is set then the grid spacing must be at least PMEGridSpacing if set or a very large default of 1 5 PMEGridSizeX lt number of grid points in x dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeX should have only small integer factors 2 3 and 5 PMEGridSizeY lt number of grid points in y dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeY should have on
104. alue no Description When enabled NAMD keeps the dimension of the unit cell in the x y plane constant while allowing fluctuations along the z axis This is not currently implemented in Berendsen s method 7 5 1 Berendsen pressure bath coupling NAMD 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 TT Default Value off Description Specifies whether or not Berendsen pressure bath coupling is active If set to on then the parameters BerendsenPressureTarget BerendsenPressureCompressibility and BerendsenPressureRelaxationTime must be set and the parameter BerendsenPressureFreq can optionally be set to control the behavior of this feature BerendsenPressureTarget lt target pressure bar gt Acceptable Values positive decimal Description Specifies target pressure for Berendsen s method A typical value would be 1 01325 bar atmospheric pressure at sea level BerendsenPressureCompressibility lt compressibility bar gt Acceptable Values positive decimal Description Specifies compressibility for Berendsen s method A typical value would be 4 57E 5 bar corresponding to liquid water The higher the compressibility the more volume will be adjusted for a given pressure difference The compressibility and the relaxation time appear only as a ratio in th
105. alue off Description Specifies whether or not Langevin piston pressure control is ac tive If set to on then the parameters LangevinPistonTarget LangevinPistonPeriod LangevinPistonDecay and LangevinPistonTemp must be set e LangevinPistonTarget lt target pressure bar gt 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
106. ameter 163 ramd rMinRamd parameter 163 readexclusions parameter 24 readpsf psfgen command 39 reassignFreq parameter 75 reassignHold parameter 75 reassignIncr parameter 75 reassignTemp parameter 15 75 rebinGrids parameter 137 ref parameter 117 ref2 parameter 117 refPositions parameter 121 127 refPositionsCol parameter 121 128 refPositionsColValue parameter 121 128 refPositionsFile parameter 121 127 refPositionsGroup parameter 128 regenerate psfgen command 37 reinitvels command 16 reloadCharges command 16 replica exchange 159 replicaID parameter 138 replicasRegistry parameter 138 replicaUpdateFrequency parameter 138 rescaleFreq parameter 75 rescaleTemp parameter 15 75 rescalevels command 16 resetpsf psfgen command 38 residue psfgen command 36 residueRange parameter 123 restartfreq parameter 21 restartname parameter 21 199 restartsave parameter 21 rigidBonds parameter 54 rigidDieOnError parameter 54 rigidIterations parameter 54 rigidTolerance parameter 54 rotateReference parameter 127 rotConsAxis parameter 91 rotConsPivot parameter 91 rotConstraints parameter 91 rotConsVel parameter 91 run command 15 runAve parameter 130 runAveLength parameter 130 runAveOutputFile parameter 130 runAveStride parameter 130 SASA parameter 64 saveFreeEnergyFile parameter 139 scnb parameter 24 seed parameter 70 segment psfgen command 35 selectConstraints parameter 56 selectC
107. and 39 XSTfile parameter 65 XSTfreq parameter 65 zeroMomentum parameter 71
108. and are included in all distributions 188 18 5 Documentation All available NAMD documentation is available for download without registration via the NAMD web site http www ks uiuc edu Research namd 189 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 C H Bennett Efficient estimation of free energy differences with monte carlo data J Comp Phys 22 245 268 1976 F C Bernstein T F Koetzle G J B Williams J E F Meyer M D Brice J R Rodgers O Kennard T Shimanouchi and M Tasumi The protein data bank A computer based archival file for macromolecular structures J Mol Biol 112 535 542 1977 T C Beutler A E Mark R C van Schaik P R Gerber and W F van Gunsteren Avoid ing singularities and numerical instabilities in free energy calculations based on molecular simulations Chem Phys Lett 222 529 539 1994 D L Beveridge and F M DiCapua Free energy via molecular simulation Applications to chemical and biomolecular systems Annu Rev Biophys Biophys 18 431 492 1989 A Bondi van der Waals volumes and radii J Phys Chem 68 441 451 1964 S Boresch and M Karplus The role
109. and colvarsInput all the parameters defining the colvars and their biases are read from the extra input file provided by colvarsConfig Hence none of the keywords described in this and the following sections are available in the NAMD main configuration The syntax of the collective variables configuration file is similar to that of the NAMD file 2 2 1 with a few important differences e certain keywords may have multiple values 108 a long value or values can be distributed across several lines by using curly braces and the opening brace must occur on the same line as the keyword after a space character or any other white space blocks defined by curly braces may be nested therefore the values of a keyword such as colvar may in turn contain simple keywords such as name and keywords with other blocks such as distance nested keywords are only meaningful within the parent keyword s block and not elsewhere when the same keyword is available within different blocks it may have different meanings for every keyword documented in the following the parent keyword defining the context block is indicated in parentheses certain keywords can be used multiple times even within the same context e g the keyword colvar as in the NAMD configuration comments can be inserted at any point using the hash sign unlike in the NAMD config the deprecated sign between a keyword and its value is not all
110. and efficient simulation method for biomolecules J Chem Phys 120 24 11919 11929 2004 E Harder V M Anisimov I V Vorobyov P E M Lopes S Y Noskov A D MacKerell and B Roux Atomic level anisotropy in the electrostatic modeling of lone pairs for a polarizable force field based on the classical drude oscillator J Chem Theor Comp 2 6 1587 1597 2006 G D Hawkins C J Cramer and D G Truhlar Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium J Phys Chem 100 19824 19839 1996 J H nin and C Chipot Overcoming free energy barriers using unconstrained molecular dynamics simulations J Chem Phys 121 2904 2914 2004 J H nin G Fiorin C Chipot and M L Klein Exploring multidimensional free energy landscapes using time dependent biases on collective variables J Chem Theory Comput 6 1 35 47 2010 T Huber A E Torda and W van Gunsteren Local elevation A method for improving the searching properties of molecular dynamics simulation Journal of Computer Aided Molecular Design 8 6 695 708 DEC 1994 G Hummer and I Kevrekidis Coarse molecular dynamics of a peptide fragment Free energy kinetics and long time dynamics computations Journal of Chemical Physics 118 23 10762 10773 JUN 15 2003 191 33 34 35 36 37 38 39 40 41 42 43 44 45
111. and molecular dynamics simulation algorithm J Chem Phys 119 6 3025 3039 2003 N Lu D A Kofke and T B Woolf Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods J Comput Chem 25 28 39 2004 Z M T P Straatsma and M J A Separation shifted scaling a new scaling method for Lennard Jones interactions in thermodynamic integration J Chem Phys 100 9025 9031 1994 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 S J Marrink A H de Vries and A E Mark Coarse grained model for semiquantitative lipid simulations J Phys Chem B 108 750 760 2004 S J Marrink H J Risselada S Yefimov D P Tieleman and A H de Vries The martini forcefield coarse grained model for biomolecular simulations J Phys Chem B 111 7812 7824 2007 J A McCammon and S C Harvey Dynamics of Proteins and Nucleic Acids Cambridge University Press Cambridge 1987 192 48 49 50 51 52 54 55 56 57 58 L Monticelli S Kandasamy X Periole and R L D T S Marrink The martini coarse grained forcefield extension to proteins J Chem Theor Comp 4 819 834 2008 A Onufriev
112. and return some geometry parameters bond angle dihedral 99 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 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 13 in radian This command takes the coordinates of the three atoms as input and returns a list of 26 00 00 os ot 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 73 73 74 in radian This command takes the coordinates of the four atoms as input and returns a list of gs se e F Each element of the list is a 3 D vector in the form of a Tcl list
113. anness of the machine on which the DCD file was written and the utility program flipdcd is also provided to reformat these files if needed The exact format of these files is very ugly but supported by a wide range of analysis and display programs The timestep is stored in the DCD file in NAMD internal units and must be multiplied by TIMEFACTOR 48 88821 to convert to fs Positions in DCD files are stored in A Velocities in DCD files are stored in NAMD internal units and must be multiplied by PDBVELFACTOR 20 45482706 to convert to A ps Forces in DCD files are stored in kcal mol A 18 3 1 5 NAMD binary files NAMD uses a trivial double precision binary file format for coordinates velocities and forces Due to its high precision this is the default output and restart format VMD refers to these files as the namdbin format The file consists of the atom count as a 32 bit integer followed by all three position or velocity components for each atom as 64 bit double precision floating point i e NXYZXYZXYZXYZ where N is a 4 byte int and X Y and Z are 8 byte doubles If the number of atoms the file contains is known then the atom count can be used to determine endianness The file readers in NAMD and VMD can detect and adapt to the endianness of the machine on which the binary file was written and the utility program flipbinpdb is also provided to reformat these files if needed Positions in NAMD binary files are stored in A Velocities in NAM
114. ant kub 0 where like the spring bond rik IF 7 gives the distance between the pair of atoms and rup is the equilibrium distance The 4 body torsion angle also known as dihedral angle potential describes the angular spring between the planes formed by the first three and last three atoms of a consecutively bonded i j k l quadruple of atoms DE t cos ny ifn gt 0 5 k py ifn 0 where 4 is the angle in radians between the 7 7 k plane and the j k l plane The integer constant n is nonnegative and indicates the periodicity For n gt 0 is the phase shift angle and k is the multiplicative constant For n 0 acts as an equilibrium angle and the units of k change to potential rad A given i j k quadruple of atoms might contribute multiple terms to the potential each with its own parameterization The use of multiple terms for a torsion angle allows for complex angular variation of the potential effectively a truncated Fourier series 42 5 1 2 Nonbonded potential energy terms The nonbonded potential terms involve interactions between all i j pairs of atoms usually ex cluding pairs of atoms already involved in a bonded term Even using a fast evaluation methods the cost of computing the nonbonded potentials dominates the work required for each time step of an MD simulation The Lennard Jones potential accounts for the weak dipole attraction between distant atoms and the hard core
115. 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 101 e tclBCArgs lt extra args for tclBC calcforces command gt Acceptable Values args Description The string or Tcl list provided by this option is appended to the tclBC calcforces command arguments This parameter may appear multiple times during a run in order to alter the parameters of the boundary potential function The script provided in tclBCScript and the calcforces procedure it defines are executed in multiple Tcl interpreters one for every processor that owns patches These tcl1BC interpreters do not share state with the Tcl int
116. ated at any distance In this scheme the cutoff parameter has a slightly different meaning for the electrostatic interactions it represents the local interaction distance or distance within which 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 7 3 4 5 2 3 Non bonded force field parameters e cutoff lt local interaction distance common to both electrostatic and van der Waals calcu lations A gt Acceptable Values positive decimal Description See Section 5 2 for more information 44 energy d cutoff distance Figure 2 Graph showing an electrostatic potential with and without the application of the shifting function gt direct at Bo every step S o cutoff 0 distance Figure 3 Graph showing an electrostatic potential when full electrostatics are used within NAMD with one curve portion calculated directly and the other calculated using PME e switching lt use switching function gt Acceptable Values on or off Default Value on Description If switching is specified to be off then a truncated cutoff is performed If switching is turned on then smoothing functions are applied to both the electrostatics and van der Waals forces For a complete description of the non bonded force parameter
117. ber which is computed by one or more instances of the following components distance distance between two groups distanceZ projection of a distance vector on an axis distanceXY projection of a distance vector on a plane distanceVec distance vector between two groups distanceDir unit vector parallel to distanceVec angle angle between three groups coordNum coordination number between two groups 114 e selfCoordNum coordination number of atoms within a group e hBond hydrogen bond between two atoms e rmsd root mean square deviation RMSD from a set of reference coordinates e eigenvector projection of the atomic coordinates on a vector e orientationAngle angle of the best fit rotation from a set of reference coordinates e tilt projection on an axis of the best fit rotation from a set of reference coordinates e gyration radius of gyration of a group of atoms e alpha a helix content of a protein segment e dihedralPC projection of protein backbone dihedrals onto a dihedral principal component Periodic components The following components returns real numbers that lie in a periodic interval e dihedral torsional angle between four groups e spinAngle angle of rotation around a predefined axis in the best fit from a set of reference coordinates In certain conditions distanceZ can also be periodic namely when periodic boundary conditions PBCs are defined in the simulation and distanceZ s axis is par
118. ble 115 Non scalar components When one of the following are used the colvar returns a value that is not a scalar number e distanceVec 3 dimensional vector of the distance between two groups e distanceDir 3 dimensional unit vector of the distance between two groups e orientation 4 dimensional unit quaternion representing the best fit rotation from a set of reference coordinates The distance between two 3 dimensional unit vectors is computed as the angle between them The distance between two quaternions is computed as the angle between the two 4 dimensional unit vectors because the orientation represented by q is the same as the one represented by q distances between two quaternions are computed considering the closest of the two symmetric images Non scalar components carry the following restrictions e Calculation of system forces outputSystemForce option is currently not implemented e Each colvar can only contain one non scalar component e Binning on a grid abf histogram and metadynamics with useGrids enabled is currently not implemented for colvars based on such components Note while these restrictions apply to individual colvars based on non scalar components no limit is set to the number of scalar colvars To compute multi dimensional histograms and PMFs use sets of scalar colvars of arbitrary size Calculating system forces In addition to the restrictions due to the type of value computed scalar or n
119. calculated in addition to the electrostatic and van der Waals forces To simulate a system using only Go forces the partial charges and Lennard Jones parameters can be set to zero in the force field files e GoParameters lt Parameter file defining Go potential gt Acceptable Values file Description File contains parameters to define the Go pairwise forces between different 165 chain types All possible chain type pairing combinations must be enumerated Chain types are defined in the GoCoordinates file The format for the GoParameters file is described in the next section e GoCoordinates lt Reference structure for Go simulation gt Acceptable Values PDB file Description PDB file contains the reference structure used to define the Go potential The file need not be the same file used to initialize the coordinates of the MD simulation however it must contain the same number of atoms in the same order as given in the structure psf and coordinates coor file Additionally the occupancy fields of the PDB file will be read to determine which chain type an individual atom belongs to and thus which pairwise Go potential to use to calculate forces By default the occupancy value of 0 0 turns off the Go potential for that particular atom e GoMethod lt controls method for storing Go contact information gt Acceptable Values lowmem or matrix Description Specifies whether the Go contacts should be calculated on the fly or stor
120. cancelling negative term the static pressure The instantaneous pressure of a simulation cell as simulated by NAMD will have mean square fluctuations according to David Case quoting Section 114 of Statistical Physics by Landau and Lifshitz of kT V 8 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 76 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 times
121. ce results show that the NAMD implementation of the Drude model maintains good parallel scalability with an increase in computational cost by not more than twice that of using a nonpolarizable force field 34 The Drude polarizable force field requires some extensions to the CHARMM force field The Drude oscillators differ from typical spring bonds only in that they have an equilibrium length of zero The Drude oscillators are optionally supplemented by a maximal bond length parameter beyond which a quartic restraining potential is also applied The force field is also extended by an anisotropic spring term that accounts for out of plane forces from a polarized atom and its covalently bonded neighbor with two more covalently bonded neighbors similar in structure to an improper bond The screened Coulomb correction of Thole is calculated between pairs of Drude oscillators that would otherwise be excluded from nonbonded interaction and optionally between non excluded nonbonded pairs of Drude oscillators that are within a prescribed cutoff distance 64 65 Also included in the Drude force field are the use of off centered massless interaction sites so called lone pairs LPs to avoid the limitations of centrosymmetric based Coulomb in teractions 27 The coordinate of each LP site is constructed based on three guide atoms The calculated forces on the massless LP must be transferred to the guide atoms preserving total force and torque
122. celerated NAMD across multiple nodes You will need either an ibverbs NAMD binary available for download or an MPI 185 NAMD binary must build Charm and NAMD as described above to make use of the InfiniBand network The use of SMP binaries is also recommended when running on multiple nodes with one process per GPU and as many threads as available cores reserving one core per process for the communication thread The CUDA NVIDIA s graphics processor programming platform code in NAMD is completely self contained and does not use any of the CUDA support features in Charm gt When building NAMD with CUDA support you should use the same Charm you would use for a non CUDA build Do NOT add the cuda option to the Charm build command line The only changes to the build process needed are to add with cuda and possibly cuda prefix to the NAMD config command line 17 11 Memory Usage NAMD has traditionally used less than 100MB of memory even for systems of 100 000 atoms With the reintroduction of pairlists in NAMD 2 5 however memory usage for a 100 000 atom system with a 12A cutoff can approach 300MB and will grow with the cube of the cutoff This extra memory is distributed across processors during a parallel run but a single workstation may run out of physical memory with a large system To avoid this NAMD now provides a pairlistMinProcs config file option that specifies the minimum number of processors that a run must u
123. ceptable Values boolean Default Value off Description When useGrids and this option are on all hills are saved to the state file in their analytic form alongside their grids This makes it possible to later use exact analytic Gaussians for rebinGrids To only keep track of the history of the added hills writeHillsTrajectory is preferable e writeHillsTrajectory lt metadynamics Write a log of new hills gt Acceptable Values boolean Default Value on Description If this option is on a logfile is written by the metadynamics bias with the name lt outputName gt colvars lt name gt hills traj which can be useful to follow the time series of the hills When multipleReplicas is on its name changes to lt outputName gt colvars lt name gt lt replicaID gt hills traj This file can be used to quickly visualize the positions of all added hills in case newHillFrequency does not coincide with colvarsRestartFrequency 10 3 3 Harmonic restraints and Steered Molecular Dynamics The harmonic biasing method may be used to enforce fixed or moving restraints including variants of Steered and Targeted MD Within energy minimization runs it allows for restrained minimiza tion e g to calculate relaxed potential energy surfaces In the context of the colvars module harmonic potentials are meant according to their textbook definition V a k a 20 Note that this differs from harmonic bond and angle potentials in common
124. cities parameter 20 BOUNDARY energy 22 parame callback command 15 cellBasisVectorl parameter 65 cellBasisVector2 parameter 65 cellBasisVector3 parameter 65 cellOrigin parameter 65 centerReference parameter 127 centers parameter 140 checkpoint command 16 closestToQuaternion parameter 122 colvars parameter 107 131 colvarsConfig parameter 107 colvarsInput parameter 108 colvarsRestartFrequency parameter 109 colvarsTrajAppend parameter 109 colvarsTrajFrequency parameter 109 COMmotion parameter 70 component Coeff parameter 125 componentExp parameter 125 consexp parameter 55 consForceConfig command 16 85 consForceFile parameter 85 consForceScaling parameter 16 85 conskcol parameter 55 conskfile parameter 55 consref parameter 55 constantForce parameter 16 85 constraints parameter 55 constraintScaling parameter 16 55 coord psfgen command 39 coordinates parameter 19 coordpdb psfgen command 40 coorfile command 16 corrFunc parameter 129 corrFuncLength parameter 130 corrFuncNormalize parameter 129 corrFuncOffset parameter 130 corrFuncOutputFile parameter 130 corrFuncStride parameter 130 corrFuncType parameter 129 corrFuncWithColvar parameter 129 cosAngles parameter 54 cutoff parameter 44 119 cutoff3 parameter 119 cwd parameter 20 cylindricalBC parameter 67 cylindricalBCAxis parameter 67 cylindricalBCCenter parameter 67 cylindricalBCexp1 parameter 68 cylindricalBCexp2
125. cl use tc1BC as described in Sec 9 11 7 1 1 Periodic boundary conditions NAMD provides periodic boundary conditions in 1 2 or 3 dimensions The following parameters are used to define these boundary conditions e cellBasisVector1 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellBasisVector2 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellBasisVector3 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellOrigin lt center of periodic cell A gt Acceptable Values position Default Value 000 Description When position rescaling is used to control pressure this location will remain constant Also used as the center of the cell for wrapped output coordinates e extendedSystem lt XSC file to read cell parameters from gt Acceptable Values file name Description In addition to coor and vel output files NAMD generates a xsc eXtended System Configuration file which contains the periodic cell parameters and extended system variables such as the strain rate in constant pressure simulations Periodic cell parameters will be read from this file if this option is pr
126. ctions calculated Let us consider a concrete example to better understand this Assume that the pairlist is built once every ten timesteps and that the cutoff distance is 8 0 Consider a pair of atoms A and B that are 8 1 apart when the pairlist is built If the pair list includes only those atoms within the cutoff distance this pair would not be included in the list Now assume that after five timesteps atoms A and B have moved to only 7 9 apart A and B are now within the cutoff distance of each other and should have their non bonded interactions calculated However because the non bonded interactions are based solely on the pair list and the pair list will not be rebuilt for another five timesteps this pair will be ignored for five timesteps causing energy not to be conserved within the system To avoid this problem the parameter pairlistdist allows the user to specify a distance greater than the cutoff distance for pairs to be included in the pair list as shown in Figure 4 Pairs that are included in the pair list but are outside the cutoff distance are simply ignored So in the above example if the pairlistdist were set to 10 0 then the atom pair A and B would be included in the pair list even though the pair would initially be ignored because they are further apart than the cutoff distance As the pair moved closer and entered the cutoff distance because the pair was already in the pair list the non bonded interactions would
127. d In phase 2 the Pi force contribution hereafter called the dEdr force is calculated as well as the partial derivative of the Born radii with GB respect to the atom positions A In phase 3 the ae are force contribution hereafter called the dEda force is calculated 62 6 3 Configuration Parameters When using GBIS user s should not use PME because it is not compatible with GBIS Periodic boundary conditions are supported but are optional User s will need to increase cutoff 16 18 A is a good place to start but user s will have to check their system s behavior and increase cutoff accordingly GBIS interactions are never excluded regardless of the type of force field used thus user s can choose any value for exclude without affecting GBIS user s should still choose exclude based on the force field as if using explicit solvent When using GBIS multiple timestepping behaves as follows the dEdr force is calculated every nonbondedFreq steps as with explicit solvent 2 is a reasonable frequency and the dEda force is calculated every fullElectFrequency steps because dEda varies more slowly than dEdr 4 is a reasonable frequency GBIS lt Use Generalized Born Implicit Solvent gt Acceptable Values on or off Default Value off Description Turns on GBIS method in NAMD solventDielectric lt dielectric of water gt Acceptable Values positive decimal Default Value 78 5 Description Defines the
128. d and the file contains all the atoms in the topology this option may be povided to set which PDB field will be used to select the reference coordinates for atoms e refPositionsColValue lt rmsd Value in the PDB column gt Acceptable Values positive decimal Description If defined this value identifies in the PDB column refPositionsCol of the file refPositionsFile which atom positions are to be read Otherwise all positions with a non zero value will be read This component returns a positive real number in A Component eigenvector projection of the atomic coordinates on a vector The block eigenvector defines the projection of the coordinates of a group of atoms or more precisely their deviations from the reference coordinates onto a vector in R where n is the number of atoms in the group The computed quantity is the total projection n 1 n p xi t Ey Y vi Ulit Xcog t 5D xP 40 i 1 i 1 where as in the rmsd component U is the optimal rotation matrix Xcog t and x feb are the centers of geometry of the current and reference positions respectively and v are the components of the vector for each atom Example choices for v are an eigenvector of the covariance matrix essential mode or a normal mode of the system It is assumed that gt vj 0 otherwise the colvars module centers the v automatically when reading them from the configuration As in the rmsd component available
129. d max values width need not be the same that for the current run This command is useful to piece together data from simulations in different regions of collective variable space or change the colvar boundary values and widths Note that it is not recommended to use it to switch to a smaller width as 133 that will leave some bins empty in the finer data grid This option is NOT compatible with reading the data from a restart file colvarsInput option of the NAMD config file e applyBias lt ABF Apply the ABF bias gt Acceptable Values boolean Default Value yes Description If this is set to no the calculation proceeds normally but the adaptive biasing force is not applied Data is still collected to compute the free energy gradient This is mostly intended for testing purposes and should not be used in routine simulations e updateBias lt ABF Update the ABF bias gt Acceptable Values boolean Default Value yes Description If this is set to no the initial biasing force e g read from a restart file or through inputPrefix is not updated during the simulation As a result a constant bias is applied This can be used to apply a custom tabulated biasing potential to any combination of colvars To that effect one should prepare a gradient file containing the biasing force to be applied negative gradient of the potential and a count file containing only values greater than fullSamples These files must match the grid parame
130. d to understand this material collective variable based calculations Sec 10 and basic Tcl programming to adapt the examples in 1ib replica umbrella and lib replica umbrella2d until further documentation and a tutorial are available This implementation is designed to be modified to implement exchanges of parameters other than temperature or via other temperature exchange methods The scripts should provide a good starting point for any simulation method requiring a number of loosely interacting systems Replica exchanges and energies are recorded in the history files written in the output directories These can be viewed with e g xmgrace output history and processed via awk or other tools There is also a script to load the output into VMD and color each frame according to replica index An example simulation folds a 66 atom model of a deca alanine helix in about 10 ns 159 replica namd is the master script for replica temperature exchange simulations To run cd example mkdir output cd output mkdir 0 12345 6 7 mpirun namd2 replicas 8 job0 conf stdout output d job0 d log mpirun namd2 replicas 8 job1 conf stdout output d job1 d log The number of MPI ranks must be a multiple of the number of replicas replicas Be sure to increment jobX for stdout option on command line show_replicas vmd is a script for loading replicas into VMD first source the replica exchange conf file and then this script then repeat fo
131. data to follow that convention by remov ing this contribution from the output gradients while applying internally the corresponding correction to ensure uniform sampling It is not allowed for colvars with multiple components e outputFreq lt ABF Frequency in timesteps at which ABF data files are refreshed gt Acceptable Values positive integer Default Value Colvar module restart frequency Description The files containing the free energy gradient estimate and sampling histogram and the PMF in one dimensional calculations are written on disk at the given time interval e historyFreq lt ABF Frequency in timesteps at which ABF history files are accumulated gt Acceptable Values positive integer Default Value 0 Description If this number is non zero the free energy gradient estimate and sampling histogram and the PMF in one dimensional calculations are appended to files on disk at the given time interval History file names use the same prefix as output files with hist appended e inputPrefix lt ABF Filename prefix for reading ABF data gt Acceptable Values list of strings Description If this parameter is set for each item in the list ABF tries to read a gradient and a sampling files named lt inputPrefix gt grad and lt inputPrefix gt count This is done at startup and sets the initial state of the ABF algorithm The data from all provided files is combined appropriately Also the grid definition min an
132. ded that the latter are appropriately accounted for in the thermodynamic cycle 14 11 3 Examples of input files for running alchemical free energy calculations The first example illustrates the use of TCL scripting for running an alchemical transformation with the FEP feature of NAMD In this calculation A is changed continuously from 0 to 1 by increments of 6A 0 1 alch On Enable alchemical simulation module alchType fep Set alchemical method to FEP alchFile ion fep File containing the information about grow alchCol X ing shrinking atoms described in column X alchOutfile ion fepout Output file containing the free energy alchOutFreq 5 Frequency at which fepOutFreq is updated alchEquilSteps 5000 Number of equilibration steps per A state set Lambda0 0 0 Starting value of A set dLambda 0 1 Increment of A i e dl while Lambda0 lt 1 0 TCL script to increment A alchLambda Lambda0 1 set lambda value set Lambda0 expr LambdaO0 dLambda 2 increment A alchLambda2 Lambda0 3 set lambda value pe 10000 4 run 10 000 MD steps The user should be reminded that by setting run 10000 10 000 MD steps will be performed which includes the preliminary fepEquilSteps equilibration steps This means that here the ensemble average of equation 57 will be computed over 5 000 MD steps Alternatively states may be declared explicitly avoiding the use of TCL scripting alchLambda 0 0 1 set alchLambda value alchLambda2 0
133. defined provides the force constant The energy unit of the constant is kcal mol while the spatial unit is that of the colvar e upperWall lt colvar Position of the upper wall gt Acceptable Values decimal Default Value upperBoundary Description Similar to lowerWal1 e upperWallConstant lt colvar Upper wall force constant kcal mol gt Acceptable Values positive decimal Description Similar to lowerWallConstant Trajectory output e outputValue lt colvar Output a trajectory for this colvar gt Acceptable Values boolean Default Value on Description If colvarsTrajFrequency is non zero the value of this colvar is written to the trajectory file every colvarsTrajFrequency steps in the column labeled lt name gt e outputVelocity lt colvar Output a velocity trajectory for this colvar gt Acceptable Values boolean 112 Default Value off Description If colvarsTrajFrequency is defined the finite difference calculated velocity of this colvar are written to the trajectory file under the label v_ lt name gt e outputEnergy lt colvar Output an energy trajectory for this colvar gt Acceptable Values boolean Default Value on Description This option applies only to extended Lagrangian colvars If colvarsTrajFrequency is defined the kinetic energy of the extended degree and freedom and the potential energy of the restraining spring are are written to the trajectory file under the labels Ek_
134. degrees others and lt k gt is a spring constant in the potential energy function U x k x tres or for dihedrals and impropers with periodicity lt n gt specified and not 0 U x k 1 cos na ref Note that x ef is only a minimum for the harmonic potential the sinusoidal potential has minima at tres 180 n i x 360 n 58 6 Generalized Born Implicit Solvent Generalized Born implicit solvent GBIS is a fast but approximate method for calculating molecular electrostatics in solvent as described by the Poisson Boltzmann equation which models water as a dielectric continuum GBIS enables the simulation of atomic structures without including explicit solvent water The elimination of explicit solvent greatly accelerates simulations this speedup is lessed by the increased computational complexity of the implicit solvent electrostatic calculation and a longer interaction cutoff These are discussed in greater detail below 6 1 Theoretical Background Water has many biologically necessary properties one of which is as a dielectric As a dielectric water screens lessens electrostatic interactions between charged particles Water can therefore be crudely modeled as a dielectric continuum In this manner the electrostatic forces of a biological system can be expressed as a system of differential equations which can be solved for the electric field caused by a collection of charges 6 1 1 Poisson Boltzmann Equation The Po
135. distribution of P A 3 In P E Ag 46 In the TI formalism the free energy is obtained from its gradient which is generally calculated in the form of the average of a force F exerted on taken over an iso surface VEA E Fee 47 Several formulae that take the form of 47 have been proposed This implementation relies partly on the classic formulation 12 and partly on a more versatile scheme originating in a work by Ruiz Montero et al 54 generalized by den Otter 19 and extended to multiple variables by Ciccotti et al 15 Consider a system subject to constraints of the form o x 0 Let v4 ief1 n be arbitrarily chosen vector fields RIN RIN verifying for all i j and k vi Ves 0 48 vi Vz Ok 0 49 then the following holds 15 OA DE vi i Vz V kel Vz vijg 50 where V is the potential energy function v can be interpreted as the direction along which the force acting on variable is measured whereas the second term in the average corresponds to the geometric entropy contribution that appears as a Jacobian correction in the classic formalism 12 Condition 48 states that the direction along which the system force on amp is measured is orthogonal to the gradient of which means that the force measured on does not act on Equation 49 implies that constraint forces are orthogonal to the directions along which the free energy gradient is measur
136. ds or processes are set to run on or not run on specific processor cores or hardware threads On Linux this can be done at the process level with the numactl utility but NAMD provides its own options for assigning threads to cores This feature is enabled by adding setcpuaffinity to the namd2 command line which by itself will cause NAMD really the underlying Charm library to assign threads processes round robin to available cores in the order they are numbered by the operating system This may not be the fastest configuration if NAMD is running fewer threads than there are cores available and consecutively numbered cores share resources such as memory bandwidth or are hardware threads on the same physical core If needed specific cores for the Charm PEs processing elements and communication threads on all SMP builds and on multicore builds when the commthread option is specified can be set by adding the pemap and if needed commap options with lists of core sets in the form lower upper stride run A single number identifies a particular core Two numbers separated by a dash identify an inclusive range lower bound and upper bound If they are followed by a colon and another number a stride that range will be stepped through in increments of the additional number Within each stride a dot followed by a run will indicate how many cores to use from that starting point For example the sequence 0 8 2 16 20 24 includes
137. e 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 7 4 3 Temperature rescaling parameters NAMD allows equilibration of a system by means of temperature rescaling Using this method all of the velocities in the system are periodically rescaled so that the entire system is set to the desired temperature The following parameters specify how often and to what temperature this rescaling is performed 74 e rescaleFreq lt number of timesteps between temperature rescaling gt Acceptable Values positive integer Description The equilibration feature of NAMD is activated by specifying the number of timesteps between each temperature rescaling If this value is given then the rescaleTemp parameter must also be given to specify the target temperature e rescaleTemp lt temperature for equilibration K gt Acceptable Values positive decimal Description The temperature to which all velocities will be rescaled every rescaleFreq timesteps This param
138. e If set to on then the parameter langevinTemp must be set and the parameters langevinFile and langevinCol can optionally be set to control the behavior of this feature e langevinTemp lt temperature for Langevin calculations K gt Acceptable Values positive decimal Description Temperature to which atoms affected by Langevin dynamics will be adjusted This temperature will be roughly maintained across the affected atoms through the addition of friction and random forces e langevinDamping lt damping coefficient for Langevin dynamics 1 ps gt Acceptable Values positive decimal Default Value per atom values from PDB file Description Langevin coupling coefficient to be applied to all atoms unless langevinHydrogen is off in which case only non hydrogen atoms are affected If not given a PDB file is used to obtain coefficients for each atom see langevinFile and langevinCol below e langevinHydrogen lt Apply Langevin dynamics to hydrogen atoms gt Acceptable Values on or off Default Value on Description If langevinDamping is set then setting langevinHydrogen to off will turn off Langevin dynamics for hydrogen atoms This parameter has no effect if Langevin coupling coefficients are read from a PDB file e langevinFile lt PDB file containing Langevin parameters gt Acceptable Values UNIX filename Default Value coordinates 73 Description PDB file to use for the Langevin coupling coefficients for each atom If th
139. e NAMD will automatically distribute threads equally among the GPUs on a node Specific GPU device IDs can be requested via the devices argument on the namd2 command line for example namd2 idlepoll p4 devices 0 2 lt configfile gt Devices are shared by consecutive threads in a process so in the above example processes 0 and 1 will share device 0 and processes 2 and 3 will share device 2 Repeating a device will cause it to be assigned to multiple master threads either in the same or different processes which is advised against in general but may be faster in certain cases In the above example one could specify devices 0 2 0 2 to cause device 0 to be shared by threads 0 and 2 etc When running on multiple nodes the devices specification is applied to each physical node separately and there is no way to provide a unique list for each node GPUs of compute capability 1 0 are no longer supported and are ignored GPUs with two or fewer multiprocessors are ignored unless specifically requested with devices While charmrun with local will preserve LD_LIBRARY_PATH normal charmrun does not You can use charmrun runscript to add the namd2 directory to LD_LIBRARY_PATH with the following executable runscript bin csh setenv LD_LIBRARY_PATH 1 h LD_LIBRARY_PATH x For example charmrun runscript runscript p24 namd2 idlepoll ppn 3 lt configfile gt An InfiniBand network is highly recommended when running CUDA ac
140. e contributions to the pressure profile Results will be recorded in the NAMD output file in lines with the format PRESSUREPROFILE ts Axx Ayy Azz Bxx Byy Bzz where ts is the timestep followed by the three diagonal components of the pressure tensor in the first slab the slab with lowest z then the next lowest slab and so forth The output will reflect the pressure profile averaged over all the steps since the last output NAMD also reports kinetic bonded and nonbonded contributions separately using the same format as the total pressure but on lines beginning with PPROFILEINTERNAL PPROFILEBONDED and PPROFILENONBONDED e pressureProfileSlabs lt Number of slabs in the spatial partition gt Acceptable Values Positive integer Default Value 10 169 Description _NAMD divides the entire periodic cell into horizontal slabs of equal thickness pressureProfileSlabs specifies the number of such slabs pressureProfileFreq lt How often to output pressure profile data gt Acceptable Values Positive integer Default Value 1 Description Specifies the number of timesteps between output of pressure profile data pressureProfileEwald lt Enable pressure profile Ewald sums gt Acceptable Values on or off Default Value off Description When enabled only the Ewald contribution to the pressure profile will be computed For trajectory analysis the recommended way to use this option is to use the NAMD Tel scripting interface as
141. e tabulated interactions for SI O O O and SI SI pairs would be specified in a parameter file as NBTABLE SI O SIO 0 0 00 SI SI SISI Each interaction type must correspond to an entry in the energy table file The table file consists of a header formatted as multiple comment lines lt number_of_tables gt lt table_spacing A gt lt maximum_distance A gt followed by number_of_tables energy tables formatted as TYPE lt interaction type name gt O lt energy kcal mol gt lt force kcal mol A gt lt table_spacing gt lt energy kcal mol gt lt force kcal mol A gt lt 2 table_spacing gt lt energy kcal mol gt lt force kcal mol A gt lt 3 table_spacing gt lt energy kcal mol gt lt force kcal mol A gt lt maximum_distance 3 table_spacing gt lt energy kcal mol gt lt force kcal mol A gt lt maximum_distance 2 table_spacing gt lt energy kcal mol gt lt force kcal mol A gt lt maximum_distance table_spacing gt lt energy kcal mol gt lt force kcal mol A gt 49 The table entry at marimum_distance will match the energy of the previous entry but have a force of zero The maximum distance must be at least equal to the nonbonded cutoff distance and entries beyond the cutoff distance will be ignored For the above example with a cutoff of 12 A the table file could look like parameters for silicon dioxide 3 0 01 14 0 TYPE SIO O 5 092449e 26 3 055469e 31 0 01 5 092449e 1
142. e Go potential e expRep 1 integer expRep Determines the expRep constant for the Go potential e sigmaRep 1 float 0 Determines the 0 constant for the Go potential in units of A e epsilonRep 1 float e P Determines the e constant for the Go potential in units of kcal mol A e cutoff 1 float cutoff Defines the Go cutoff distance for this particular pairwise chain in units of A e Optional restriction 1 integer Determines if interactions between the i and i integer adjacent residue should be excluded Multiple restriction between adjacent residues can be defined within a chaintype Each additional new restriction is given on its own line Each pairwise chaintype should be written in its own block of text with each entry given its own line It is recommended that individual pairwise potential be separated by a blank line 167 14 Runtime Analysis 14 1 Pair interaction calculations NAMD supportes the calculation of interaction energy calculations between two groups of atoms When enabled pair interaction information will be calculated and printed in the standard output file on its own line at the same frequency as energy output The format of the line is PAIR INTERACTION STEP step VDW_FORCE fx fy fz ELECT_FORCE fx fy fz The displayed force is the force on atoms in group 1 and is units of kcal mol For trajectory analysis the recommended way to use this set of options is to use the
143. e dynamics so a larger compressibility is equivalent to a smaller relaxation time BerendsenPressureRelaxationTime lt relaxation time fs gt Acceptable Values positive decimal Description Specifies relaxation time for Berendsen s method If the instantaneous pres sure did not fluctuate randomly during a simulation and the compressibility estimate was exact then the inital pressure would decay exponentially to the target pressure with this time constant Having a longer relaxation time results in more averaging over pressure measure ments and hence smaller fluctuations in the cell volume A reasonable choice for relaxation time would be 100 fs The compressibility and the relaxation time appear only as a ratio in the dynamics so a larger compressibility is equivalent to a smaller relaxation time BerendsenPressureFreq lt how often to rescale positions gt Acceptable Values positive multiple of nonbondedFrequency and fullElectFrequency Default Value nonbondedFrequency or fullElectFrequency if used Description Specifies number of timesteps between position rescalings for Berendsen s method Primarily to deal with multiple timestepping integrators but also to reduce cell volume fluctuations cell rescalings can occur on a longer interval This could reasonably be between 1 and 20 timesteps but the relaxation time should be at least ten times larger 7 5 2 Nos Hoover Langevin piston pressure control NAMD provides constant pre
144. e exclusions in PARM file and will automatically generate them according to the exclusion policy specified by exclude e scnb lt VDW 1 4 scaling factor gt Acceptable Values decimal gt 1 0 Default Value 2 0 Description Same meaning as SCNB in AMBER Note that in NAMD 1 4 vdw inter actions are DIVIDED by scnb whereas 1 4 electrostatic interactions are MULTIPLIED by 1 4scaling So 1 4scaling should be set to the inverse of SCEE value used in AMBER Caveat 1 Polarizable parameters in AMBER are not supported 2 NAMD does not support the 10 12 potential terms in some old AMBER versions When non zero 10 12 parameter is encountered in PARM file NAMD will terminate 3 NAMD has several exclusion policy options defined by exclude The way AMBER dealing with exclusions corresponds to the scaled1 4 in NAMD So for simulations using AMBER force field one would specify exclude scaled1 4 in the configuration file and set 1 4scaling to the inverse value of SCEE as would be used in AMBER 24 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
145. e files are only required for communication and may be deleted after a new NAMD run is started with a different outputName e replicaID lt metadynamics Set the identifier for this replica gt Acceptable Values string Description If multipleReplicas is on this option sets a unique identifier for this replica All replicas should use identical collective variable configurations except for the value of this option e replicasRegistry lt metadynamics Multiple replicas database file gt Acceptable Values UNIX filename Default Value lt name gt replica_files txt Description If multipleReplicas is on this option sets the path to the replicas database file e replicaUpdateFrequency lt metadynamics How often hills are communicated between replicas gt Acceptable Values positive integer Default Value newHillFrequency Description If multipleReplicas is on this option sets the number of steps after which each replica re reads the other replicas files The lowest meaningful value of this number is newHillFrequency If access to the file system is significantly affecting the simulation performance this number can be increased at the price of reduced synchronization between replicas Values higher than colvarsRestartFrequency may not improve performance sig nificantly e dumpPartialFreeEnergyFile lt metadynamics Periodically write the contribution to the PMF from this replica gt Acceptable Values boolean De
146. e repeated for as many times as the values of psfSegID psfSegID lt atom group PSF segment identifier gt Acceptable Values space separated list of strings max 4 characters Description This option sets the PSF segment identifier for of atomNameResidueRange Multiple values can be provided which can correspond to different instances of atomNameResidueRange in the order of their occurrence This option is not needed when non PSF topologies are used by NAMD atomsFile lt atom group PDB file name for atom selection gt Acceptable Values string Description This option selects atoms from the PDB file provided and adds them to the group according to the value in the column atomsCol Note the set of atoms PDB file provided must match the topology atomsCol lt atom group PDB column to use for the selection gt Acceptable Values X Y Z 0 or B Description This option specifies which column in atomsFile is used to determine the atoms to be included in the group 126 e atomsColValue lt atom group Value in the PDB column gt Acceptable Values positive decimal Description If defined this value in atomsCol identifies of atomsFile which atoms are to be read otherwise all atoms with a non zero value will be read e dummyAtom lt atom group Dummy atom position A gt Acceptable Values x y z triplet Description This option makes the group a virtual particle at a fixed position in space This is useful e g
147. eA A ek a 12 3 Locally enhanced sampling 12 3 1 Structure generation a 12 3 2 Simulation Aye spe wae a BAA De lee el oe eo 12 4 Replica exchange simulations e 12 5 Random acceleration molecular dynamics simulations 13 Hybrid MD Go Simulation 13 1 Hybrid MD Go model 2 20 0 0 020 0000020 a 13 2 Hybrid MD Go considerations e 13 3 Configuration file modifications 2 2 ee 13 4 GoParameter format po s sa a 44 4 8 8 Re ee RE a A ee 14 Runtime Analysis 14 1 Pair interaction calculations 2 oaa ee 14 2 Pressure profile calculations 2 ee 15 Translation between NAMD and X PLOR configuration parameters 16 Sample configuration files 17 Running NAMD 17 1 Individual Windows Linux Mac OS X or Other Unix Workstations 17 2 Windows Clusters and Workstation Networks o e 02005 17 3 Linux Clusters with InfiniBand or Other High Performance Networks 17 4 Linux or Other Unix Workstation Networks 0 02 0 2 02 00 17 5 Shared Memory and Network Based Parallelism SMP Builds OCTA OD 28 A ets aes Mech ad Fehr iin snake ae ek Tt SGL AMIR UV ina ok hol Kone Sa eh GA OA a ee ee eS 17 8 IBM POWER Clusters 2 eate ao e o a a ee 17 9 GRUESA eG ee Soe de ks PH a Ree Pee A ey A a ee eee RaR 17 10CUDA GPU Acceleration 2 na a eA a ee 17 11Memory Usage elas laa fala a a bee 2 wae 17 12Improving Parallel Scaling 2
148. eates 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 38 Arguments lt contert gt Context ID returned by psfcontext Context At any time psfcontext eval lt context gt lt commands gt y Purpose Evaluates lt commands gt in the specified context returning to the current context on exit This should be totally robust returning to the orignal context in case of errors and preventing its deletion when nested Arguments lt contert gt Context ID returned by psfcontext create lt commands gt Script to be executed in the specified context Context At any time psfcontext stats Purpose Returns the total numbers of contexts that have been created and destroyed This is useful for checking if a script is leaking contexts Arguments Context At any time writepsf charmm x plor cmap nocmap lt file name gt Purpose Write out structure information as PSF file A simplified session log is listed in the REMARKS section of the PSF file Arguments cha
149. ectric X PLOR Parameter EPS Dielectric constant e NAMD Parameter exclude X PLOR Parameter NBXMod Both parameters specify which atom pairs to exclude from non bonded interactions The ability to ignore explicit exclusions is not present within NAMD thus only positive values of NBXMod have NAMD equivalents These equivalences are NBXMod 1 is equivalent to exclude none no atom pairs excluded NBXMod 2 is equivalent to exclude 1 2 only 1 2 pairs excluded NBXMod 3 is equivalent to exclude 1 3 1 2 and 1 3 pairs excluded NBXMod 4 is equivalent to exclude 1 4 1 2 1 3 and 1 4 pairs excluded NBXMod 5 is equivalent to exclude scaled1 4 1 2 and 1 3 pairs excluded 1 4 pairs modified 173 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 timeste
150. ed so that the measurement is effectively performed on unconstrained 131 degrees of freedom In NAMD constraints are typically applied to the lengths of bonds involving hydrogen atoms for example in TIP3P water molecules parameter rigidBonds section 5 6 1 In the framework of ABF F is accumulated in bins of finite size 0 thereby providing an estimate of the free energy gradient according to equation 47 The biasing force applied along the colective variables to overcome free energy barriers is calculated as FABF _ V A 51 where V A denotes the current estimate of the free energy gradient at the current point in the collective variable subspace As sampling of the phase space proceeds the estimate Vp Ais progressively refined The biasing force introduced in the equations of motion guarantees that in the bin centered around the forces acting along the selected collective variables average to zero over time Eventually as the undelying free energy surface is canceled by the adaptive bias evolution of the system along is governed mainly by diffusion Although this implementation of ABF can in principle be used in arbitrary dimension a higher dimension collective variable space is likely to result in sampling difficulties Most commonly the number of variables is one or two ABF requirements on collective variables 1 Only linear combinations of colvar components can be used in ABF calculations 2 Avail
151. ed by your sysadmin or by a ssh authorized_keys file in your home directory You should confirm that you can run ssh hostname pwd or rsh hostname pwd without typing a password before running NAMD Contact your local sysadmin if you have difficulty setting this up If you are unable to use rsh or ssh then add setenv CONV DAEMON to your script and run charmd or charmd_faceless which produces a log file on every node You should now be able to try running NAMD as charmrun namd2 p lt procs gt lt configfile gt If this fails or just hangs try adding the verbose option to see more details of the startup process You may need to specify the full path to the namd2 binary Charmrun will start the number of processes specified by the p option cycling through the hosts in the nodelist file as 181 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
152. ed from QM calculations e drudeBondConst lt Drude oscillator restraining force constant gt Acceptable Values positive decimal Description If drudeBondConst is defined an additional quartic restraining potential is applied to a Drude oscillator if its length exceeds drudeBondLen The recommended value is 40000 fitted from QM calculations e drudeNbTholeCut lt nonbonded Thole interaction radius A gt Acceptable Values positive decimal Description If drudeNbTholeCut is defined the screened Coulomb correction of Thole is also calculated for non excluded nonbonded pairs of Drude oscillators that are within this radius of interaction The recommended value is 5 0 A for a high concentration gt 1 M ionic solution or otherwise leave it 0 5 5 MARTINI Residue Based Coarse Grain Forcefield The MARTINI forcefield for residue based coarse grain models allows simulation of several tens of atoms as only several large coarse grained particles 45 46 48 In the MARTINI model each protein residue is represented by a backbone bead and usually one or more sidechain beads When preparing MARTINI simulations it is important to include only those dihedrals specified by the forcefield Using the auto dihedrals or regenerate dihedrals feature of psfgen will create dihedrals for all possible sets of four bonded atoms This is incorrect for MARTINI and will result in energy jumps because the dihedral potential function is degenerate fo
153. ed from symmetryLastFullStep to symmetryLastStep e symmetryk lt Constant for harmonic restraining forces gt Acceptable Values Positive value Description Harmonic force constant Scaled down by number of atoms in the monomer If this setting is omitted the value in the occupancy column of the pdb file specified by symmetrykFile will be used as the constant for that atom This allows the user to specify the constant on a per atom basis e symmetrykFile lt pdb containing per atom force constants gt Acceptable Values Path to pdb file Description pdb where the occupancy column specifies the per atom force constants If using overlapping symmetry groups you must include one additional symmetrykfile per symmetryFile e symmetryScaleForces lt Scale symmetry restraints over time gt Acceptable Values on or off Default Value off Description If turned on the harmonic force applied by the symmetry re straints will linearly evolve with each time step based on symmetryFirstFullStep and symmetryLastFullStep e symmetryFile lt File for symmetry information gt Acceptable Values Path to PDB file 92 Description Restrained atoms are those whose occupancy O is nonzero in the sym metry pdb file The file must contain the same number of atoms as the structure file The value in the occupancy column represent the symmetry group the atom belongs to These symmetry groups are used for denoting monomers of the same type These g
154. ed in a matrix respectively In most cases lowmem will be sufficient However for smaller systems the matrix does offer a slight performance speedup in terms of wall time Variable is only used if GoForcesOn is on The following sections describe the format of the GoParameter file 13 4 GoParameter format When running a Go simulation the atoms are partitioned into chains according to the occupancy value given in the GoCoordinates file For every possible pairwise combination between chains a Go potential is defined by the following equations Let p be the pairwise distance between atoms i and j in the reference structure If ri is less than the Go cutoff distance the pairwise potential between atoms i and j is given by a a ont b VaolTig or GUS ae gt F a where ge is given as 2 a oe If es is greater than the Go cutoff distance the pair wise potential between atoms i and j is given by rep o 2 Vaolrij P o expRep Ae Ene UJ For each pairwise chain combination the following parameters are needed to define the Go potential e chaintypes 2 floats first_chain second_chain Defines the pairwise chain interaction e epsilon 1 float e Determines the e constant of the Go potential in units of kcal mol t A 166 e exp_a 1 integer a Determines the a constant for the Go potential e exp_b 1 integer b Determines the b constant for th
155. ed systems There are other fast evaluation methods that approximate the contribution to the long range electrostatic terms that require O N or O N log N computational cost depending on the method 5 2 Non bonded interactions NAMD has a number of options that control the way that non bonded interactions are calculated These options are interrelated and can be quite confusing so this section attempts to explain the behavior of the non bonded interactions and how to use these parameters 5 2 1 Van der Waals interactions The simplest non bonded interaction is the van der Waals interaction In NAMD van der Waals interactions are always truncated at the cutoff distance specified by cutoff The main option that effects van der Waals interactions is the switching parameter With this option set to on a smooth switching function will be used to truncate the van der Waals potential energy smoothly at the cutoff distance A graph of the van der Waals potential with this switching function is shown in Figure 1 If switching is set to off the van der Waals energy is just abruptly truncated at the cutoff distance so that energy may not be conserved 43 switchdist cutoff Pe TA CR AR COE A H A RRA SAA energy distance Figure 1 Graph of van der Waals potential with and without the application of the switching function With the switching function active the potential is smoothly reduced to 0 at the cutoff distance Witho
156. ee below By default the force constant is changed smoothly over a total of targetNumSteps steps This is useful to introduce or remove re straints in a progressive manner If targetNumStages is set to a nonzero value the change is performed in discrete stages lasting targetNumSteps steps each This second mode may be used to compute the conformational free energy change associated with the restraint within the FEP or TI formalisms For convenience the code provides an estimate of the free energy derivative for use in TI A more complete free energy calculation particularly with regard to convergence analysis while not handled by the colvars module can be performed by post processing the colvars trajectory if colvarsTrajFrequency is set to a suitably small value It should be noted however that restraint free energy calculations may be handled more efficiently by an indirectly route through the determination of a PMF for the restrained coordinate 20 140 targetForceExponent lt Exponent in the time dependence of the force constant gt Acceptable Values decimal equal to or greater than 1 0 Default Value 1 0 Description Sets the exponent a in the function used to vary the force constant as a function of time The force is varied according to a coupling parameter A raised to the power a ky ko A ky ko where ko ky and k are the initial current and final values of the force constant The parameter A evolves linearly
157. efault 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 19 Default Value off Description Specifies whether or not the parameter file s are in CHARMM format X PLOR format is the default for parameter files Caveat The information about multiplicity of dihedrals will be obtained directly from the parameter file and the full multiplicity will be used same behavior as in CHARMM If the PSF file originates from X PLOR consecutive multiple entries for the same dihedral indicating the dihedral multiplicity for X PLOR will be ignored e velocities lt velocity PDB file gt Acceptable Values UNIX filename Description The PDB file containing the initial velocities for all atoms in the simulation This is typically a restart file or final velocity file written 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 e binvelocities lt binary velocity file gt Acceptable Values UNIX filename
158. egers Description The last timestep to apply adaptive tempering adaptTempCgamma lt dynamic bin averaging constant gt Acceptable Values Non negative real number Default Value 0 1 Description The calculation of the mean energy for a given bin is weighted by a factor of 1 Cgamma samples to damp out old statistics Setting Cgamma to zero restores the use of a standard arithmetic mean to calculate the mean energy for each bin adaptTempRandom lt assign random temperature if we step out of range gt Acceptable Values on or off Default Value off Description If set to on and the temperature steps out of adaptTempTmin adaptTempTmax a random temperature in that range is assigned Otherwise the previous temperature is kept 157 12 3 Locally enhanced sampling Locally enhanced sampling LES 53 57 58 increases sampling and transition rates for a portion of a molecule by the use of multiple non interacting copies of the enhanced atoms These enhanced atoms experience an interaction electrostatics van der Waals and covalent potential that is divided by the number of copies present In this way the enhanced atoms can occupy the same space while the multiple instances and reduces barriers increase transition rates 12 3 1 Structure generation To use LES the structure and coordinate input files must be modified to contain multiple copies of the enhanced atoms psfgen provides the multiply command for this purpose NAM
159. en Drude particle LP hydrogen hydrogen The atoms in the water molecules should be constrained rigidBonds water with use of the SETTLE algorithm recommended useSettle on Ex plicitly setting the water model waterModel swm4 is optional e drude lt Perform integration of Drude oscillators gt Acceptable Values on or off Default Value off 52 Description The integration uses a dual Langevin thermostat to freeze the Drude oscil lators while maintaining the warm degrees of freedom at the desired temperature Must also enable the Langevin thermostat If drude is set to on then drudeTemp must also be defined e drudeTemp lt temperature for freezing the Drude oscillators K gt Acceptable Values non negative decimal Description For stability the Drude oscillators must be kept at a very cold termpature Using a Langevin thermostat it is possible to set this temperature to 0 K e drudeDamping lt damping coefficient for Drude oscillators 1 ps gt Acceptable Values positive decimal Description The Langevin coupling coefficient to be applied to the Drude oscillators If not given drudeDamping is set to the value of langevinDamping e drudeBondLen lt Drude oscillator bond length beyond which to apply restraint A gt Acceptable Values positive decimal Description An additional quartic restraining potential is applied to a Drude oscilla tor if its length exceeds drudeBondLen The recommended value is 0 2 A fitt
160. en on the command line 3 2 2 Output files e outputname lt output file prefix gt Acceptable Values UNIX filename prefix Description At the end of every simulation NAMD writes two files one containing the final coordinates and another containing the final velocities of all atoms in the simulation This option specifies the file prefix for these two files as well as the default prefix for trajectory and restart files The position coordinates will be saved to a file named as this prefix with coor 20 appended The velocities will be saved to a file named as this prefix with vel appended For example if the prefix specified using this option was tmp output then the two files would be tmp output coor and tmp output vel binaryoutput lt use binary output files gt Acceptable Values yes or no Default Value yes Description Enables the use of binary output files If this option is not set to no then the final output files will be written in binary rather than PDB format Binary files preserve more accuracy between NAMD restarts than ASCII PDB files but the binary files are not guaranteed to be transportable between computer architectures The atom count record is used to detect wrong endian files which works for most atom counts The utility program flipbinpdb is provided to reformat these files if necessary restartname lt restart files prefix gt Acceptable Values UNIX filename prefix Default Value outputname re
161. ent context resids Return a list of resids for the molecule in the current context residue Return the residue name of the residue in the given segment with the given resid atoms Return a list of atoms for the given segment with the given resid coordinates Return x y z coordinates for the given atom first Returns the name of the patch that was applied to the beginning of the specified segment last Returns the name of the patch that was applied to the end of the specified segment lt segment ID gt Unique name for segment 1 4 characters lt commands gt Sequence of commands in Tcl syntax to build the primary structure of the segment including auto first last residue pdb etc Context After topology definitions and residue aliases May call multiple times Structure information is generated at the end of every segment command auto angles dihedrals none Purpose Override default settings 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
162. enter cylindricalBCexp1 lt exponent for first potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for first boundary potential The only likely values to use are 2 and 4 cylindricalBCr2 lt radius for second boundary condition A gt Acceptable Values positive decimal Description Distance at which the second potential of the boundary conditions takes effect along the non axis plane of the cylinder If this parameter is defined then cylindricalBC12 and spericalBCk2 must also be defined cylindricalBC12 lt radius for second boundary condition A gt Acceptable Values positive decimal Description Distance at which the second potential of the boundary conditions takes effect along the cylinder axis If this parameter is defined then cylindricalBCr2 and spericalBCk2 must also be defined cylindricalBCk2 lt force constant for second potential gt Acceptable Values non zero decimal Description Force constant for the second harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center cylindricalBCexp2 lt exponent for second potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for second boundary potential The only likely values to use are 2 and 4 7 2 Energy Minimization 7 2 1 Conjugate gradient parameters The default minimizer uses a sophisticated co
163. ents of a membrane s center of mass by distanceZ In the general case the user should determine according to which type of calculation is being performed whether wrapA11 or wrapWater can be enabled e Performance issues While NAMD spreads the calculation of most interaction terms over many computational nodes the colvars calculation is not parallelized This has two conse quences additional load on the master node where the colvar calculation is performed and additional communication between nodes NAMD s latency tolerant design and dynamic load balancing alleviate these factors still under some circumstances significant performance im pact may be observed especially in the form of poor parallel scaling To mitigate this as a general guideline the size of atom groups involved in colvar components should be kept small unless necessary to capture the relevant degrees of freedom 10 2 5 Statistical analysis of individual collective variables When the global keyword analysis is defined in the configuration file calculations of statistical properties for individual colvars can be performed At the moment several types of time correlation functions running averages and running standard deviations are available e corrFunc lt colvar Calculate a time correlation function gt Acceptable Values boolean Default Value off Description Whether or not a time correlaction function should be calculated for this colvar e corrFu
164. ents the number of timesteps between atom reassignments For more details on non bonded force evaluation see Section 5 2 splitPatch lt how to assign atoms to patches gt Acceptable Values position or hydrogen Default Value hydrogen Description When set to hydrogen hydrogen atoms are kept on the same patch as their parents allowing faster distance checking and rigid bonds hgroupCutoff A lt used for group based distance testing gt Acceptable Values positive decimal Default Value 2 5 Description This should be set to twice the largest distance which will ever occur between a hydrogen atom and its mother Warnings will be printed if this is not the case This value is also added to the margin margin lt extra length in patch dimension A gt Acceptable Values positive decimal Default Value 0 0 Description An internal tuning parameter used in determining the size of the cubes of space with which NAMD uses to partition the system The value of this parameter will not change the physical results of the simulation Unless you are very motivated to get the very best possible performance just leave this value at the default pairlistMinProcs lt min procs for pairlists gt Acceptable Values positive integer Default Value 1 Description Pairlists may consume a large amount of memory as atom counts densities and cutoff distances increase Since this data is distributed across processors it is normally only
165. erpreter used for tclForces or config file parsing The calcforces procedure is passed as arguments the current timestep a unique flag which is non zero for exactly one Tcl interpreter in the simulation that on the processor of patch zero and any arguments provided to the most recent tclBCArgs option The unique flag is useful to limit printing of messages since the command is invoked on multiple processors The print vecadd vecsub vecscale getbond getangle getdihedral anglegrad and dihedralgrad commands described under tclForces are available at all times The wrapmode lt mode gt command available in the tclBCScript or the calcforces procedure determines how coordinates obtained in the calcforces procedure are wrapped around periodic boundaries The options are e patch default the position in NAMD s internal patch data structure requires no extra calculation and is almost the same as cell e input the position corresponding to the input files of the simulation e cell the equivalent position in the unit cell centered on the 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 mextatom 4 to itera
166. esearch institution or corporation as necessary to the terms and conditions of the license agreement All parts of the information must be understood and agreed to as part of completing the form Completion of the form is required before software access is granted Pay particular attention to the authorized requester requirements above and be sure that the form submission is authorized by the duly responsible person UNIVERSITY OF ILLINOIS NAMD MOLECULAR DYNAMICS SOFTWARE LICENSE AGREEMENT Upon execution of this Agreement by the party identified below Licensee The Board of Trustees of the University of Illinois Illinois on behalf of The Theoretical 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 no
167. esent ignoring the above parameters e XSTfile lt XST file to write cell trajectory to gt Acceptable Values file name Default Value outputname xst Description _NAMD can also generate a xst eXtended System Trajectory file which contains a record of the periodic cell parameters and extended system variables during the simulation If XSTfile is defined then XSTfreq must also be defined e XSTfreq lt how often to append state to XST file gt Acceptable Values positive integer 65 Description Like the DCDfreq option controls how often the extended system configura tion will be appended to the XST file e wrapWater lt wrap water coordinates around periodic boundaries gt Acceptable Values on or off Default Value off Description Coordinates are normally output relative to the way they were read in Hence if part of a molecule crosses a periodic boundary it is not translated to the other side of the cell on output This option alters this behavior for water molecules only e wrapAll lt wrap all coordinates around periodic boundaries gt Acceptable Values on or off Default Value off Description Coordinates are normally output relative to the way they were read in Hence if part of a molecule crosses a periodic boundary it is not translated to the other side of the cell on output This option alters this behavior for all contiguous clusters of bonded atoms e wrapNearest lt use nearest image to cell origin when
168. eter is valid only if rescaleFreq has been set 7 4 4 Temperature reassignment parameters NAMD allows equilibration of a system by means of temperature reassignment Using this method all of the velocities in the system are periodically reassigned so that the entire system is set to the desired temperature The following parameters specify how often and to what temperature this reassignment is performed e reassignFreq lt number of timesteps between temperature reassignment gt Acceptable Values positive integer Description The equilibration feature of NAMD is activated by specifying the num ber of timesteps between each temperature reassignment If this value is given then the reassignTemp parameter must also be given to specify the target temperature e reassignTemp lt temperature for equilibration K gt Acceptable Values positive decimal Default Value temperature if set otherwise none Description The temperature to which all velocities will be reassigned every reassignFreq timesteps This parameter is valid only if reassignFreq has been set e reassignIncr lt temperature increment for equilibration K gt Acceptable Values decimal Default Value 0 Description In order to allow simulated annealing or other slow heating cooling protocols reassignIncr will be added to reassignTemp after each reassignment Reassignment is carried out at the first timestep The reassignHold parameter may be set to limit the final tempera
169. eviation gt Acceptable Values UNIX filename Default Value lt name gt runave dat Description The running average and standard deviation are saved in this file 10 3 Biasing and analysis methods All of the biasing and analysis methods implemented abf harmonic histogram and metadynamics recognize the following options e name lt colvar bias Identifier for the bias gt Acceptable Values string 130 Default Value lt type of bias gt lt bias index gt Description This string is used to identify the bias or analysis method in output messages and to name some output files e colvars lt colvar bias Collective variables involved gt Acceptable Values space separated list of colvar names Description This option selects by name all the colvars to which this bias or analysis will be applied 10 3 1 Adaptive Biasing Force For a full description of the Adaptive Biasing Force method see reference 18 For details about this implementation see references 29 and 30 When publishing research that makes use of this functionality please cite references 18 and 30 An alternate usage of this feature is the application of custom tabulated biasing potentials to one or more colvars See inputPrefix and updateBias below ABF is based on the thermodynamic integration TI scheme for computing free energy profiles The free energy as a function of a set of collective variables Esdieltn is defined from the canonical
170. exp GAA _i41 59 14 1 runs 11 4 2 Thermodynamic Integration When running TI free energy calculations the elec_dU dl and vdW_dU dl1 values reported in ti0utFile are the derivatives of the internal energy with respect to A i e ae for electro statics and van der Waals respectively dU d1 values are averages over the last tiOutFreq steps Cumulative averages for each component are reported alongside in the _avg columns The electrostatics and vdW are separated following a partition scheme that is the appear ing and the disappearing atoms are accounted for separately Partition 1 contains those atoms whose interactions are switched up as increases i e flagged with 1 in the alchFile Partition 2 represents those atoms whose interactions are switched down as A increases i e flagged with 1 AA values for each component are obtained by integrating from A 0 to 1 using the respective ELEC VDW LAMBDA listed for each partition after the title Analysis is handled by the NAMD_ti script available from http www ks uiuc edu Research namd utilities Although the output format of NAMD_ti pl may appear to lend itself easily to interpretation of the individual contributions to the free energy total elec and vdW for each partition this is rarely appropriate as these values are path dependent For example an output such as 10 LA KASSSSSEE 3 ASS 0 0 0 2
171. fault Value on Description When multipleReplicas is on tje file lt outputName gt pmf contains the combined PMF from all replicas Enabling this option will produce an additional file lt outputName gt partial pmf which can be useful to quickly monitor the contribution of each replica to the PMF The requirements for this option are the same as dumpFreeEnergyFile The following options may be useful for applications that go beyond the direct application of metadynamics for a calculation of a PMF 138 e name lt metadynamics Name of this metadynamics instance gt Acceptable Values string Default Value meta rank number Description This option sets the name for this metadynamics instance While it is not advisable to use more than one metadynamics instance within the same simulation this allows to distinguish each instance from the others If there is more than one metadynamics instance the name of this bias is included in the metadynamics output file names such as dumpFreeEnergyFile e saveFreeEnergyFile lt metadynamics Keep all the PMF files gt Acceptable Values boolean Default Value off Description When dumpFreeEnergyFile and this option are on the step number is included in the file name Activating this option can be useful to follow more closely the convergence of the simulation by comparing PMFs separated by short times e keepHills lt metadynamics Write each individual hill to the state file gt Ac
172. file Non targeted atoms are ignored The beta column of targetted atoms is used to designate non overlapping constraint domains Forces will be calculated for atoms within a domain separately from atoms of other domains e TMDFirstStep lt first TMD timestep gt Acceptable Values Positive integer Default Value 0 Description e TMDLastStep lt last TMD timestep gt Acceptable Values Positive integer Description TMD forces are applied only between TMDFirstStep and TMDLastStep The target RMSD evolves linearly in time from the initial to the final target value 94 e TMDInitialRMSD lt target RMSD at first TMD step gt Acceptable Values Non negative value in A Default Value from coordinates Description In order to perform TMD calculations that involve restarting a previous NAMD run be sure to specify TMDInitialRMSD with the same value in each NAMD input file and use the NAMD parameter firstTimestep in the continuation runs so that the target RMSD continues from where the last run left off e TMDFinalRMSD lt target RMSD at last TMD step gt Acceptable Values Non negative value in A Default Value 0 Description If no TMDInitialRMSD is given the initial RMSD will be calculated at the first TMD step TMDFinalRMSD may be less than or greater than TMDInitialRMSD depending on whether the system is to be steered towards or away from a target structure respectively Forces are applied only if RMS t is betwween TMDInitialRMSD and
173. for the harmonic restraints feature of NAMD For historical reasons the terminology of harmonic constraints has been carried over from X PLOR This feature allows a harmonic restraining force to be applied to any set of atoms in the simulation constraints lt are constraints active gt Acceptable Values on or off Default Value off Description Specifies whether or not harmonic constraints are active If it is set to off then no harmonic constraints are computed If it is set to on then harmonic constraints are calculated using the values specified by the parameters consref conskfile conskcol and consexp 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 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 conskfile lt PDB file containing force constant values gt Acceptable Values UNIX filename Description PDB file to use for force constants for harmonic constraints conskcol lt column of PDB file cont
174. force fields where the factor of one half is typically omitted resulting in a non standard definition of the force constant The restraint energy is reported by NAMD under the MISC title A harmonic restraint is set up by a harmonic block which may contain in addition to the standard option colvars the following keywords e forceConstant lt harmonic Scaled force constant kcal mol gt Acceptable Values positive decimal 139 Default Value 1 0 Description This defines a scaled force constant for the harmonic potential To ensure consistency for multidimensional restraints it is divided internally by the square of the specific width for each colvar involved which is 1 by default so that all colvars are effectively dimensionless and of commensurate size For instance setting a scaled force constant of 10 kcal mol acting on two colvars an angle with a width of 5 degrees and a distance with a width of 0 5 A will apply actual force constants of 0 4 kcal molxdegree for the angle and 40 kcal mol A for the distance centers lt harmonic Initial harmonic restraint centers gt Acceptable Values space separated list of colvar values Description The centers equilibrium values of the restraint are entered here The number of values must be the number of requested colvars Each value is a decimal number if the corresponding colvar returns a scalar a x y z triplet if it returns a unit vector or a vector and a
175. g to the minimum image convention If this parame ter is set to yes PBC will be ignored and the distance between the coordinates as maintained internally will be used This is only useful in a limited number of special cases e g to de scribe the distance between remote points of a single macromolecule which cannot be split across periodic cell boundaries and for which the minimum image distance might give the wrong result because of a relatively small periodic cell e oneSiteSystemForce lt distance Measure system force on group 1 only gt Acceptable Values boolean Default Value no Description If this is set to yes the system force is measured along a vector field see equation 50 in section 10 3 1 that only involves atoms of group1 This option is only useful for ABF or custom biases that compute system forces See section 10 3 1 for details The value returned is a positive number in A ranging from 0 to the largest possible interatomic distance within the chosen boundary conditions with PBCs the minimum image convention is used unless the forceNoPBC option is set Component distanceZ projection of a distance vector on an axis ThedistanceZ block defines a distance projection component which can be seen as measuring the distance between two groups projected onto an axis or the position of a group along such an axis The axis can be defined using either one reference group and a constant vector or dynamically based o
176. her than computing a tri cubic interpolation of the potential from which the force is then computed analytically Gridforce Lite computes force as a linear interpolation This method also increases the memory required by Gridforce Note that Gridforce Lite is incompatible with use of the mgridforcecont 123 keywords and with non uniform grids 9 4 Moving Constraints Moving constraints feature works in conjunction with the Harmonic Constraints see an appropriate section of the User s guide The reference positions of all constraints will move according to rt Fo Ut 30 A velocity vector Y movingConsVel needs to be specified The way the moving constraints work is that the moving reference position is calculated ev ery integration time step using Eq 30 where is in A timestep and t is the current timestep i e firstTimestep plus however many timesteps have passed since the beginning of NAMD run Therefore one should be careful when restarting simulations to appropriately update the firstTimestep parameter in the NAMD configuration file or the reference position specified in the reference PDB file NOTE NAMD actually calculates the constraints potential with U k x zo and the force with F dk x xo where d is the exponent consexp The result is that if one specifies some 89 22 20 4 Potential E 1 a l
177. 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 patch grid remains the same size The workaround is to increase the margin parameter so that the simulation starts with fewer larger patches
178. in a NAMD configuration file Section 2 2 3 lists the parameters which are required to run a basic simulation Section 15 describes the relation between specific NAMD and X PLOR dynamics options Several sample NAMD configuration files are shown in section 16 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 14 Some keywords require several lines of data These are generally implemented to either allow the data to be read from a file keyword filename or to be included inline using Tcl style braces keyword lots of data The specification of the keywords is case insensitive so that any combination of upper and lower case letters will have the same meaning Hence DCDfile and dcdfile are equivalent The capitalization in the values however may be important Some values indicate file names in which capitalization is critical Other values such as on or off are case insensitive
179. in parallel the provided non MPI binaries should still work for serial runs The provided charmrun program for these platforms is only a script that attempts to translate charmrun options into mpirun options but due to the diversity of MPI libraries it often fails to work 17 4 Linux or Other Unix Workstation Networks The same binaries used for individual workstations as described above other than pure multicore builds and MPI builds can be used with charmrun to run in parallel on a workstation network The only difference is that you must provide a nodelist file listing the machines where namd2 processes should run for example group main host brutus host romeo The group main line defines the default machine list Hosts brutus and romeo are the two machines on which to run the simulation Note that charmrun may run on one of those machines or charmrun may run on a third machine All machines used for a simulation must be of the same type and have access to the same namd2 binary By default the rsh command is used to start namd2 on each node specified in the nodelist file You can change this via the CONV_RSH environment variable i e to use ssh instead of rsh run setenv CONV_RSH ssh or add it to your login or batch script You must be able to 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 install
180. ing large numbers of extra terms to be specified with minimal impact on parallel scalability Extra bonded terms do not have to duplicate normal bonds angles dihedrals but each extra bond angle dihedral should only involve nearby atoms If the atoms involved are too far apart a bad global bond count will be reported in parallel runs Extra bonded terms are enabled via the following options e extraBonds lt enable extra bonded terms gt Acceptable Values on or off Default Value off Description Specifies whether or not extra bonded terms are present e extraBondsFile lt file containing extra bonded terms gt Acceptable Values file Description File containing extra bonded terms May be repeated for multiple files The extra bonds file s should contain lines of the following formats e bond lt atom gt lt atom gt lt k gt lt ref gt e angle lt atom gt lt atom gt lt atom gt lt k gt lt ref gt e dihedral lt atom gt lt atom gt lt atom gt lt atom gt lt k gt lt ref gt e dihedral lt atom gt lt atom gt lt atom gt lt atom gt lt k gt lt n gt lt ref gt e improper lt atom gt lt atom gt lt atom gt lt atom gt lt k gt lt ref gt e improper lt atom gt lt atom gt lt atom gt lt atom gt lt k gt lt n gt lt ref gt e lt comment gt 57 In all cases lt atom gt is a zero based atom index the first atom has index 0 lt ref gt is a reference distance in A bond or angle in
181. ion Specifies acceleration in kcal mol A amu to be applied during RAMD step ramd rMinRamd lt Set threshold for distance traveled RAMD gt Acceptable Values positive decimal Default Value 0 01 Description Specifies a threshold value for the distance in Angstroms traveled by the ligand in 1 RAMD block In pure RAMD simulations the direction of the acceleration is changed if the ligand traveled less than rMinRamd Ain the evaluated block In combined RAMD MD simulations a switch from a RAMD block to a standard MD block is applied if the ligand traveled more than rMinRamd Ain the evaluated block ramd rMinMd lt Set threshold for distance traveled in MD gt Acceptable Values positive decimal Description Specifies a threshold value for the distance in Angstroms traveled by accel erated atoms in 1 standard MD block In combined RAMD MD simulations a switch from a standard MD block to a RAMD block is applied according to the criteria described in the note below Required if mdStep is not 0 ignored if mdSteps is 0 ramd forceQutFreq lt Set frequency of RAMD forces output gt Acceptable Values positive integer Must be divisor of both ramdSteps and mdSteps Default Value 0 Description Every forceOutFreq steps detailed output of forces will be written ramd maxDist lt Set center of mass separation gt Acceptable Values positive decimal Default Value 50 Description Specifies the distance i
182. ion or report will be supplied to Illinois at the addresses listed below in Contact Information 7 Should Licensee wish to make commercial use of the Software Licensee will contact Illinois namd ks uiuc edu to negotiate an appropriate license for such use Commercial use includes 1 integration of all or part of the Software into a product for sale lease or license by or on behalf of Licensee to third parties or 2 distribution of the Software to third parties that need it to commercialize product sold or licensed by or on behalf of Licensee 8 Government Rights Because substantial governmental funds have been used in the devel opment of NAMD any possession use or sublicense of the Software by or to the United States government shall be subject to such required restrictions 9 NAMD is being distributed as a research and teaching tool and as such 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
183. is parameter is not specified then the PDB file specified by coordinates is used e langevinCol lt column of PDB from which to read coefficients gt Acceptable Values X Y Z 0 or B Default Value 0 Description Column of the PDB file to use for 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 7 4 2 Temperature coupling parameters NAMD is capable of performing temperature coupling in which forces are added or reduced to simulate the coupling of the system to a heat bath of a specified temperature This capability is based on that implemented in X PLOR which is detailed in the X PLOR User s Manual 10 e tCouple lt perform temperature coupling gt Acceptable Values on or off Default Value off Description Specifies whether or not temperature coupling is active If set to on then the parameter tCoupleTemp must be set and the parameters tCoupleFile and tCoupleCol can optionally be set to control the behavior of this feature e tCoupleTemp lt temperature for heat bath K gt Acceptable Values positive decimal Description Temperature to which atoms affected by temperature coupling will be ad justed This temperature will be roughly maintained across the affected atoms through the addition of forces e tCoupleFile lt PDB file with tCouple parameters gt Acceptable Values UNIX filenam
184. isson Boltzmann equation PBE is a nonlinear equation which solves for the electrostatic field W 7 based on the position dependent dielectric e r the position dependent accessibility of position F to the ions in solution A F the solute charge distribution p F and the bulk charge density c of ion q While this equation does exactly solve for the electrostic field of a charge distribution in a dielectric it is very expensive to solve and therefore not suitable for molecular dynamics 6 1 2 Generalized Born The Generalized Born GB equation is an approximation of the PBE It models atoms as charged spheres whose internal dielectric is lower than that of the environment The screening which each atom 7 experiences is determined by the local environment the more atom 7 is surrounded by other atoms the less it s electrostatics will be screened since it is more surrounded by low dielectric this property is called one atom descreening another Different GB models calculate atomic descreening differently Descreening is used to calculate the Born radius a of each atom The Born radius of an atom measures the degree of descreening A large Born radius represents small screening strong electric field as if the atom were in vacuum A small Born radius represents large screening weak electric field as if the atom were in bulk water The next section describes how the Born radius is calculated and how it is used to calculate elec
185. iteSystemForce lt distanceZ distanceXY Measure system force on group main only gt Acceptable Values boolean Default Value no Description If this is set to yes the system force is measured along a vector field see equation 50 in section 10 3 1 that only involves atoms of main This option is only useful for ABF or custom biases that compute system forces See section 10 3 1 for details This component returns a number in A whose range is determined by the chosen boundary conditions For instance if the z axis is used in a simulation with periodic boundaries the returned value ranges between b 2 and b 2 where b is the box length along z this behavior is disabled if forceNoPEC is set Component distanceXY modulus of the projection of a distance vector ona plane The distanceXY block defines a distance projected on a plane and accepts the same keywords as distanceZ i e main ref either ref2 or axis and oneSiteSystemForce It returns the norm of the projection of the distance vector between main and ref onto the plane orthogonal to the axis The axis is defined using the axis parameter or as the vector joining ref and ref2 see distanceZ above Component distanceVec distance vector between two groups The distanceVec block defines a distance vector component which accepts the same keywords as distance groupl group2 and forceNoPEC Its value is the 3 vector joining the centers of mass of group1 and group
186. ition 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 91 Description Angular velocity of rotation degrees timestep 9 6 Symmetry Restraints Symmetry restraints are based on symmetrical relationships between monomers Defined monomers are transformed to overlap and an average position for each atom is calculated After the average structure is transformed back a harmonic force is calculated which drives each monomer to the average e symmetryRestraints lt Are symmetry restraints active gt Acceptable Values on or off Default Value off Description Should Symmetry constraining forces be applied to the system If symmetry restraints are enabled symmetryk and symmetryFile must be defined in the input file as well See symmetryk entry for details e symmetryFirstFullStep lt First step to apply full harmonic force gt Acceptable Values Non negative integer Default Value symmetryFirstStep Description Force constant symmetryk linearly increased from symmetryFirstStep to symmetryFirstFullStep e symmetryLastFullStep lt Last step to apply full harmonic force gt Acceptable Values Non negative integer Default Value symmetryLastStep Description Force constant symmetryk linearly decreas
187. ity with which the constraints move There are two major differences between SMD and harmonic constraints e In harmonic constraints each tagged atom is harmonically constrained to a reference point which moves with constant velocity In SMD it is the center of mass of the tagged atoms which is constrained to move with constant velocity 95 e In harmonic constraints each tagged atom is constrained in all three spatial dimensions In SMD tagged atoms are constrained only along the constraint direction unless the optional SMDk2 keyword is used The center of mass of the SMD atoms will be harmonically constrained with force constant k SMDk to move with velocity v SMDVel in the direction 7 SMDDir SMD thus results in the following potential being applied to the system z 2 Ue EN E Sk vt A t By al 33 Here t Nisdt where Ni is the number of elapsed timesteps in the simulation and dt is the size of the timestep in femtoseconds Also R t is the current center of mass of the SMD atoms and Ro is the initial center of mass as defined by the coordinates in SMDFile Vector is normalized by NAMD before being used Optionally one may also specify a transverse force constant k2 SMDk2 The potential then becomes gt is sh ut R t Fo A She ee fa to Ro 1 34 In this case the force constant k controls the potential parallel to the pulling direction 7 while the transverse force consta
188. l Beyond 20 2 sparser sampling is justified as dE dA is not changing quickly aa a A a ek EY Schematics of the aMD method When the original potential thick line falls below a threshold energy E dashed line a boost potential is added The modified energy profiles thin lines have smaller barriers separating adjacent energy basins 10 90 1 Introduction NAMD is a parallel molecular dynamics program for UNIX platforms designed for high performance simulations in structural biology This document describes how to use NAMD its features and the platforms on which it runs The document is divided into several sections Section 1 gives an overview of NAMD Section 2 lists the basics for getting started Section 3 describes NAMD file formats Section 4 explains PSF file generation with psfgen Section 5 presents the potential functions non bonded interactions and full electrostatics Section 6 explains Generalized Born implicit solvent simulations Section 7 lists standard minimization and dynamics parameters Section 8 lists performance tuning parameters Section 9 explains user defined forces conformation change calculations Section 10 describes collective variable based calculations Section 11 explains alchemical free energy calculations Section 12 presents accelerated sampling methods Section 14 lists runtime analysis options Section 15 provides hints for X PLOR users Section 16 provides sample configuration fi
189. l be the product of the two values mgridforcepotfile lt tag gt lt grid potential file name gt Acceptable Values UNIX file name Description File specifying the grid size coordinates and potential values mgridforcevolts lt tag gt lt grid potential units in eV charge gt Acceptable Values yes or no Default Value no Description If set the grid potential values are expressed in eV Otherwise values are in kcal mol charge mgridforcescale lt tag gt lt scale factor for grid potential gt Acceptable Values Vector of decimals scale scale scale Default Value 111 Description Scale factor applied to the grid potential values mgridforcecont1 lt tag gt lt Is grid continuous in the direction of the first basis vector gt Acceptable Values yes or no Default Value no Description By specifying that the grid is continuous in a direction atoms outside of the grid will be affected by a force determined by interpolating based on the values at the edge of the grid with the values of the corresponding edge of the periodic image of the grid The current size of the simulation box is taken into account so that as the simulation box size fluctuates the force on an atom outside of the grid varies continuously until it re enters the opposite edge of the grid If the grid is not continuous in this direction the interpolated force on atoms near the edge of the grid is calculated so that it continuously approaches zero
190. l generate an error and stop The parser will sometimes not tolerate correct GROMACS files or fail to detect errors in badly formatted files e NAMD does not support all the types of bond potentials that exist in GROMACS but approximates them with harmonic or sinusoidal potentials e NAMD does not read periodic box lengths in the coordinate file They must be explicitly specified in the NAMD configuration file 27 4 Creating PSF Structure Files The psfgen structure building tool consists of a portable library of structure and file manipulation routines with a Tcl interface Current capabilities include e reading CHARMM topology files e reading psf files in X PLOR NAMD format e extracting sequence data from single segment PDB files e generating a full molecular structure from sequence data e applying patches to modify or link different segments e writing NAMD and VMD compatible PSF structure files e 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
191. le and dihedral restraints Generalized Born Implicit Solvent 6 1 Theoretical Background 0 a 6 1 1 Poisson Boltzmann Equation 6 1 2 Generalized Born 2 e pe aE OE n aD E eE A a 6 1 3 Generalized Born Equations eee ee eee 0 2 3s Phase Calculation ui Poet tne he Boe a Has Ban AA Ree 6 3 Configuration Parameters oaoa Standard Minimization and Dynamics Parameters 7A Boundary Conditions space noie ponr a a p eek a OR 7 1 1 Periodic boundary conditions 0 0 0 0 002 eee ee eee 7 1 2 Spherical harmonic boundary conditions 0000 7 1 3 Cylindrical harmonic boundary conditions 00 72 Energy Minimization 2 saana e a a a aa aa ee 7 2 1 Conjugate gradient parameters 2 0 e a 7 2 2 Velocity quenching parameters e Gio OYDAN OS Le E A e ae Sea a A AAA E Shy Ee 19 1 Fimestep Para Mebers ni A o RO A A A 1327 Umi tialiZatiOn a a A A a a bA 7 3 3 Conserving momentum 0 00002 eee ee ee ee 7 3 4 Multiple timestep parameters 02 0002 eee eee eee 7 4 Temperature Control and Equilibration 2 2 0204 7 4 1 Langevin dynamics parameters 7 4 2 Temperature coupling parameters 2 000 020004 7 4 3 Temperature rescaling parameters 0 2 00 0002000 e 7 4 4 Temperature reassignment parameters 0 0 0 0 ee ee eee 7 4 5 Lowe Andersen dynamics parameters 0 2 0
192. le lt coordinate trajectory output file gt Acceptable Values UNIX filename Default Value outputname dcd Description The binary DCD position coordinate trajectory filename This file stores the trajectory of all atom position coordinates using the same format binary DCD as X PLOR If DCDfile is defined then DCDfreq must also be defined 21 DCDfreq lt timesteps between writing coordinates to trajectory file gt Acceptable Values positive integer Description The number of timesteps between the writing of position coordinates to the trajectory file The initial positions will not be included in the trajectory file Positions in DCD files are stored in A DCDUnitCell lt write unit cell data to dcd file gt Acceptable Values yes or no Default Value yes if periodic cell Description If this option is set to yes then DCD files will contain unit cell information in the style of Charmm DCD files By default this option is enabled if the simulation cell is periodic in all three dimensions and disabled otherwise velDCDfile lt velocity trajectory output file gt Acceptable Values UNIX filename Default Value outputname veldcd Description The 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 velDCDfreq lt timesteps between writing velocities to trajectory file g
193. le average described earlier 12 2 Adaptive Tempering Adaptive tempering is akin to a single copy replica exchange method for dynamically updating the simulation temperature The temperature T is a new random variable in the range T min Tmax that is governed by the equation dE dT E E T 1 T sqrt 2 T where is Gaussian white noise The effect is that when the potential energy for a given structure is lower than the so far calculated average energy the temperature is lowered Conversely when the current energy is higher than the average energy the temperature is raised The effect is faster conformational sampling to find minimum energy structures The method is implemented exactly as described by 155 Zhang and Ma in J Chem Phys 132 244101 2010 using Equation 18 of their paper to calculate the average energy at a given temperature from the histogram of energies The dynamic temperature is realized either by changing the temperature of the Langevin ther mostat or by velocity rescaling 12 2 1 NAMD parameters The following parameters are used to adaptive tempering e adaptTempMD lt Is adaptive tempering active gt Acceptable Values on or off Default Value off Description Specifies whether or not adaptive tempering is used If set to on then the following parameters are required to be set either all of adaptTempTmin adaptTempTmax adaptTempBins adaptTempDt or adaptTempInFile but not both e ada
194. les Section 17 gives details on running NAMD Section 18 gives details on installing NAMD 1 1 NAMD and molecular dynamics simulations Molecular dynamics MD simulations compute atomic trajectories by solving equations of motion numerically using empirical force fields such as the CHARMM force field that approximate the actual atomic force in biopolymer systems Detailed information about MD simulations can be found in several books such as 1 47 In order to conduct MD simulations various computer programs have been developed including X PLOR 10 and CHARMM 9 These programs were originally developed for serial machines Simulation of large molecules however require enormous computing power One way to achieve such simulations is to utilize parallel computers In recent years distributed memory parallel computers have been offering cost effective computational power NAMD was designed to run efficiently on such parallel machines for simulating large molecules NAMD is particularly well suited to the increasingly popular Beowulf class PC clusters which are quite similar to the workstation clusters for which is was originally designed Future versions of NAMD will also make efficient use of clusters of multi processor workstations or PCs NAMD has several important features 11 e Force Field Compatibility The force field used by NAMD is the same as that used by the programs CHARMM 9 and X PLOR 10 This force field includes loc
195. lists the available colvar components 10 2 3 defines how to combine existing components to create new types of colvars 10 2 4 documents how to define in a compact way atom groups which are used by most components 10 2 5 lists the available option for runtime statistical analysis of the colvars 110 10 3 lists the available methods to perform biased simulations and multidimensional analysis ABF harmonic restraint histogram and metadynamics 10 2 Declaring and using collective variables Each collective variable colvar is defined as a combination of one or more individual quantities called components see Figure 6 In most applications only one is needed in this case the colvar and its component may be identified In the configuration file each colvar is created by the keyword colvar followed by its configu ration options usually between curly braces colvar Each component is defined within the the colvar block with a specific keyword that identifies the functional form for example distance defines a component of the type distance between two atom groups To obtain the value of the colvar r its components q r are summed with the formula le Do calal 36 1 where each component appears with a unique coefficient c 1 0 by default the positive integer exponent n 1 by default For information on setting these parameters see 10 2 3 10 2 1 General collective variable options
196. 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 REM REM REM REM REM REM REM REM REM REM 1 NTITLE ARKS original generated structure x plor psf file ARKS 4 patches were applied to the molecule ARKS topology 1LOV_autopsf temp top ARKS segment P1 first NTER last CTER auto angles dihedrals ARKS segment 01 first NONE last NONE auto none ARKS segment Wi first NONE last NONE auto none ARKS defaultpatch NTER P1 1 ARKS defaultpatch CTER P1 104 ARKS patch DISU P1 10 P1 2 ARKS patch DISU P1 103 P1 6 1704 NATOM 1 P1 1 ALA N NH3 0 300000 14 0070 0 All patches that were applied explicitely using the patch command are listed following the keyword patch but the patches that result from default patching like the first and last patches 40 of a segment are marked as defaultpatch Further the segment based patching rules are listed along with the angle dihedral autogeneration rules 41 5 Force Field Parameters 5 1 Potential energy functions Evaluating the force is the most computationally demanding part of molecular dynamics The force is the negative gradient of a scalar potential energy function F VUC 1 and for systems of biomolecules this potential function involves the summing
197. loses the file The coorfile command is not available on the Cray T3E Force and energy analysis are especially useful in the context of pair interaction calculations see Sec 14 1 for details as well as the example scripts in Sec 16 Please note that while NAMD has traditionally allowed comments to be started by a appear ing anywhere on a line Tcl only allows comments to appear where a new statement could begin With Tcl config file parsing enabled all shipped binaries both NAMD and Tcl comments are allowed before the first run command At this point only pure Tcl syntax is allowed In addition 16 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 2 2 3 Required NAMD configuration parameters The following parameters are required for every NAMD simulation e nu
198. 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 56 e fixedAtomsCol lt column of PDB containing fixed atom parameters gt Acceptable Values X Y Z 0 or B Default Value 0 Description Column of the PDB file to use for the containing fixed atom parameters for each atom The coefficients can be read from any floating point column of the PDB file A value of 0 indicates that the atom is not fixed 5 6 4 Extra bond angle and dihedral restraints Additional bond angle and dihedral energy terms may be applied to system allowing secondary or tertiary structure to be restrained for example Extra bonded terms are not considered part of the molecular structure and hence do not alter nonbonded exclusions The energies from extra bonded terms are included with the normal bond angle and dihedral energies in NAMD output All extra bonded terms are harmonic potentials of the form U x k 1x 2 ye except dihedrals and impropers with a non zero periodicity specified which use U x k 1 cos nx tref The only difference between dihedrals and impropers is the output field that their potential energy is added to The extra bonded term implementation shares the parallel implementation of regular bonded terms in NAMD allow
199. lt atomname gt Name of target atom lt x y z gt Coordinates to be assigned Context After structure has been generated 39 4 5 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 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 0 for atoms with guessed coordinates and 1 for atoms with no coordinate data available coordinates are set to 0 for these atoms Arguments lt file name gt PDB file to be written Context After structure and coordinates are complete Example of a Session Log The command writepsf prints a simple session log as REMARKS at the beginning of the PSF file The
200. lt name gt and Ep lt name gt e outputSystemForce lt colvar Output a system force trajectory for this colvar gt Acceptable Values boolean Default Value off Description If colvarsTrajFrequency is defined and all components support its cal culation the total system force on this colvar i e the projection of all interatomic forces except constraint forces on this colvar see equation 50 in section 10 3 1 are written to the trajectory file under the label fs_ lt name gt The physical unit for this force is kcal mol divided by the colvar unit e outputAppliedForce lt colvar Output an applied force trajectory for this colvar gt Acceptable Values boolean Default Value off Description If colvarsTrajFrequency is defined the total force applied on this colvar by biases within the colvar module are written to the trajectory under the label fa_ lt name gt The physical unit for this force is kcal mol divided by the colvar unit Extended Lagrangian e extendedLagrangian lt colvar Add extended degree of freedom gt Acceptable Values boolean Default Value off Description Adds a fictitious particle to be coupled to the colvar by a harmonic spring The fictitious mass and the force constant of the coupling potential are derived from the parameters extendedTimeConstant and extendedFluctuation described below Biasing forces on the colvar are applied to this fictitious particle rather than to the atom
201. ltis et al Given a peptide or protein segment of N residues each with Ramachandran angles and pi dPCA rests on a variance covariance analysis of the 4 N 1 variables cos w1 sin w1 cos 2 sin da cos dy sin dy Note that angles and wy have little impact on chain conformation and are therefore discarded following the implementation of dPCA in the analysis software Carma For a given principal component eigenvector of coefficients k 1 lt i lt s m 1 the projection of the current backbone conformation is N 1 E y Kan 3 cos 1 kan 2 sin Wn Kan 1 cos n 1 kan sin n 41 45 n 1 124 dihedralPC expects the same parameters as the alpha component for defining the relevant residues residueRange and psfSegID in addition to the following e vectorFile lt dihedralPC File containing dihedral PCA eigenvector s gt Acceptable Values file name Description A text file containing the coefficients of dihedral PCA eigenvectors on the cosine and sine coordinates The vectors should be arranged in columns as in the files output by Carma e vectorNumber lt dihedralPC File containing dihedralPCA eigenvector s gt Acceptable Values positive integer Description Number of the eigenvector to be used for this component 10 2 3 Linear and polynomial combinations of components Any set of components can be combined within a colvar provided that they return the same type of values scalar u
202. lue set by the user Together with upperBoundary 111 and width it provides initial parameters to define grids of values for the colvar This op tion is not available for those colvars that return non scalar values i e those based on the components distanceDir or orientation e upperBoundary lt colvar Upper boundary of the colvar gt Acceptable Values decimal Description Similarly to lowerBoundary defines the highest possible or allowed value e expandBoundaries lt colvar Allow biases to expand the two boundaries gt Acceptable Values boolean Default Value off Description If defined biasing and analysis methods may keep their own copies of lowerBoundary and upperBoundary and expand them to accommodate values that do not fit in the initial range Currently this option is used by the metadynamics bias 10 3 2 to keep all of its hills fully within the grid Note this option cannot be used when the initial boundaries already span the full period of a periodic colvar Boundary potentials walls e lowerWall lt colvar Position of the lower wall gt Acceptable Values decimal Default Value lowerBoundary Description Defines the value below which a lower bounding restraint on the colvar is applied in the form of a half harmonic potential lowerBoundary e lowerWallConstant lt colvar Lower wall force constant kcal mol gt Acceptable Values positive decimal Description If lowerWall or lowerBoundary is
203. lues in the subgrid Subgrids in turn may have subgrids of their own which may have subgrids of their own etc A non uniform grid file takes the form of a special comment block followed by multiple normal grid definitions The special comment block defines the grid hierarchy and consists of comments beginning with namdnugrid An example follows namdnugrid version 1 0 namdnugrid maingrid subgrids count 2 namdnugrid subgrid 1 generation 1 min x1 y1 z1 max x2 y2 z2 subgrids count 2 namdnugrid subgrid 2 generation 2 min x3 y3 z3 max x4 y4 z4 subgrids count 0 namdnugrid subgrid 3 generation 2 min x5 y5 z5 max x6 y6 z6 subgrids count 0 namdnugrid subgrid 4 generation 1 min x7 y7 z7 max x8 y8 z8 subgrids count 0 H HH H H HF HF The maingrid is described by the number of subgrids Subgrids are additionally described by a subgrid number a generation number which should be one higher than the generation of its super grid and min and max attributes which describe the location of the subgrid within its supergrid In this example the maingrid has two subgrids subgrid 1 and subgrid 4 labeled generation 1 The first of these subgrids has two subgrids of its own generation 2 Notice that subgrids are described immediately after their supergrid The min and max attributes are given in units of grid cells of the supergrid For example a subgrid with min O O O max 1 1 1 would redefine 8 cells of its supergrid the space between gridpoints 0 0 0
204. ly forces individually to a potentially large number of atoms use tc1BC instead as described in Sec 9 11 The following configuration parameters are used to enable the Tcl interface e tclForces lt is Tcl interface active gt Acceptable Values on or off Default Value off Description Specifies whether or not Tcl interface is active If it is set to off then no Tcl code is executed If it is set to on then Tcl code specified in tclForcesScript parameters is executed e tclForcesScript lt input for Tcl interface gt Acceptable Values file or script Description Must contain either the name of a Tcl script file or the script itself between and may include multiple lines This parameter may occur multiple times and scripts will be executed in order of appearance The script s should perform any required initialization on the Tcl interpreter including requesting data needed during the first timestep and define a procedure calcforces to be called every timestep At this point only low level commands are defined In the future this list will be expanded Current commands are e print lt anything gt This command should be used instead of puts to display output For example print Hello World e atomid lt segname gt lt resid gt lt atomname gt Determines atomid of an atom from its segment residue and name For example atomid br 2 N e addatom lt atomid gt Request coordinates of this atom for next
205. ly 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 Default Value larger of x and y grid sizes up to all available processors Description For best performance on some systems and machines it may be necessary to restrict the amount of parallelism used Experiment with this parameter if your parallel performance is poor when PME is used FFTWEstimate lt Use estimates to optimize FFT gt Acceptable Values yes or no Default Value no Description Do not optimize FFT based on measurements but on FF TW rules of thumb This reduces startup time but may affect performance FFTWUseWisdom lt Use FF TW wisdom archive file gt Acceptable Values yes or no Default Value yes Description Try to reduce startup time when possible by reading FFTW wisdom from a file and saving wisdom generated by performance measurements to the same file for future use This will reduce startup time when running the same size PME grid on the same number of processors as a previous run using the same file FFTWWisdomFile lt name of file for FFTW wisdom archive gt Acceptable Values file name Default Value
206. m a conventional molec ular dynamics simulation 31 24 67 17 39 32 One of the most recent metadynamics was first designed as a stepwise algorithm which may be roughly described as an adaptive umbrella sampling 39 and was later made continuous over time 33 This implementation provides only he latter version which is the most commonly used 135 In metadynamics the external potential on the colvars 1 2 n is U lt t Nev o Ep2 Vineta amp y W exp 64 52 i 1 2 2 t 6t 26t dE that is Vineta is a history dependent potential which acts on the current values of the colvars and depends parametrically on the previous values of the colvars It is constructed as a sum of Nev dimensional repulsive Gaussian hills with a height W their centers are located at the previously explored configurations dt 20t and they extend by approximately 20 in the direction of the i th colvar As the system evolves according to the underlying potential of mean force A incremented by the metadynamics potential Vneta new hills will tend to accumulate in the regions with a lower effective free energy A A Veta That is the probability of having a given system configuration being explored and thus a hill being added there is proportional to exp Ale KBT which tends to a nearly flat histogram when the simulation is continued until the s
207. margin 0 stepspercycle 20 integrator timestep 1 0 output outputenergies 10 outputtiming 100 binaryoutput no molecular system coordinates output bpti pdb output outputname output bpti dcdfreq 1000 protocol temperature 0 reassignFreq 1000 reassignTemp 25 reassignIncr 25 reassignHold 300 script minimize 1000 run 20000 33 4 3 Building solvent around a protein The following script illustrates how psfgen and VMD can be used together to add water around a protein structure It assumes you already have a psf and pdb file for your protein as well as a box of water which is large enough to contain the protein For more information on how atomselections can be used within VMD scripts see the VMD User s Guide proc addwater psffile pdbfile watpsf watpdb Create psf pdb files that contain both our protein as well as a box of equilibrated water The water box should be large 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
208. may use loops variables etc as you would in a VMD or NAMD script You may use psfgen interactively but we expect it to be run most often with a script file redirected to standard input The second form is as a Tcl package which can be imported into any Tcl application including VMD All the commands available to the standalone version of psfgen are available to the Tcl package using psfgen within VMD lets you harness VMD s powerful atom selection capability as well as instantly view the result of your structure building scripts Examples of using psfgen both with and without VMD are provided in this document Generating PSF and PDB files for use with NAMD will typically consist of the following steps 1 Preparing separate PDB files containing individual segments of protein solvent etc before running psfgen 2 Reading in the appropriate topology definition files and aliasing residue and atom names found in the PDB file to those found in the topology files This will generally include selecting a default protonation state for histidine residues 3 Generating the default structure using segment and pdb commands 4 Applying additional patches to the structure 5 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
209. me 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 70 7 3 3 Conserving momentum e zeroMomentum lt remove center of mass drift due to PME gt Acceptable Values yes or no Default Value no Description If enabled the net momentum of the simulation and any resultant drift is removed before every full electrostatics step This correction should conserve energy and have minimal impact on parallel scaling This feature should only be used for simulations that would conserve momentum except for the slight errors in PME Features such as fixed atoms harmonic restraints steering forces and Langevin dynamics do not conserve momentum use in combination with these features should be considered experimental Since the momentum correction is delayed enabling outputMomenta will show a slight nonzero linear momentum but there should be no center of mass drift 7 3 4 Multiple timestep parameters To further reduce the cost of computing full electrostatics NAMD uses a multiple timestepping integration scheme In this scheme the total force acting on each atom is broken i
210. method that improves the conformational space sampling by reducing energy barriers separating different states of a system The method modifies the potential energy landscape by raising energy wells that are below a certain threshold level while leaving those above this level unaffected As a result barriers separating adjacent energy basins are reduced allowing the system to sample conformational space that cannot be easily accessed in a classical MD simulation Please include the following two references in your work using the NAMD implementation of aMD e Accelerated Molecular Dynamics A Promising and Efficient Simulation Method for Biomolecules D Hamelberg J Mongan and J A McCammon J Chem Phys 120 11919 11929 2004 e Implementation of Accelerated Molecular Dynamics in NAMD Y Wang C Harrison K Schulten and J A McCammon Comp Sci Discov 4 015002 2011 12 1 1 Theoretical background In the original form of aMD 26 when the system s potential energy falls below a threshold energy E a boost potential is added such that the modified potential V r is related to the original potential V r via V r V r AV r 60 where AV r is the boost potential AV r 0 V r gt E 61 2 wae V r lt E As shown in the following figure the threshold energy E controls the portion of the potential surface affected by the boost while the acceleration factor determines the shape of the modified p
211. mics biases histogram uses parameters from the colvars to define its grid The grid ranges from lowerBoundary to upperBoundary and the bin width is set by the width parameter 142 11 Alchemical Free Energy Methods Alchemical free energy calculations model the physically impossible but computationally realizable process of gradually mutating a subset of atoms of a system from one state to another through a series of intermediate steps Two alternative methods for alchemical calculation of free energies from molecular dynamics simulation are available in NAMD Free energy perturbation FEP and thermodynamic integration TI 11 1 Theoretical Background Free energy differences can be obtained through four different routes i probability densities ii free energy perturbation iii thermodynamic integration or iv nonequilibrium work ap proaches 14 Within NAMD alchemical transformations are modeled following the second and the third routes both of which rely upon the use of a general extent parameter often referred to as the coupling parameter 6 44 35 36 for the description of chemical changes in the molecular systems between the reference and the target states 11 1 1 The dual topology paradigm In a typical alchemical transformation setup involving the alteration of one chemical species into an alternate one in the course of the simulation the atoms in the molecular topology can be classified into three groups i a gr
212. min zmin list xmax ymax zmax 4 4 List of Commands e topology list lt file name gt Purpose Read in molecular topology definitions from file Arguments lt file name gt CHARMM format topology file list Lists all currently specified topology files residues Return a list of the known residue topologies patches Return a list of the known residue patches Context Beginning of script before segment May call multiple times e pdbalias residue lt alternate name gt lt real name gt Purpose Provide translations from residues found in PDB files to proper residue names read in from topology definition files Proper names from topology files will be used in generated PSF and PDB files This command also exists under the deprecated name alias Arguments lt alternate name gt Residue name found in PDB file lt real name gt Residue name found in topology file Context Before reading 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 curr
213. mperature Description Temperature used for calculating the coupling force constant of the extended coordinate see extendedFluctuation and if needed as a target temperature for extended Langevin dynamics see extendedLangevinDamping This should normally be left at its default value extendedLangevinDamping lt colvar Damping factor for extended Langevin dynamics ps gt Acceptable Values positive decimal Default Value 0 0 Description If this is non zero the extended degree of freedom undergoes Langevin dy namics at temperature extendedTemp The friction force is minus extendedLangevinDamping times the velocity This might be useful in cases where the extended dynamics tends to become unstable because of resonances with other degrees of freedom Only use when strictly neces sary as it adds viscous friction potentially slowing down diffusive sampling and stochastic noise increasing the variance of statistical measurements 10 2 2 Collective variable components Each colvar is defined by one or more components typically only one Each component consists of a keyword identifying a functional form and a definition block following that keyword specifying the atoms involved and any additional parameters cutoffs reference values The types of the components used in a colvar determine the properties of that colvar and which biasing or analysis methods can be applied In most cases the colvar returns a real num
214. msteps page 70 e coordinates page 19 e structure page 19 e parameters page 19 e exclude page 46 e outputname page 20 e one of the following three temperature page 70 velocities page 20 binvelocities page 20 These required parameters specify the most basic properties of the simulation In addition it is highly recommended that pairlistdist be specified with a value at least one greater than cutoff 17 3 Input and Output Files NAMD was developed to be compatible with existing molecular dynamics packages especially the packages X PLOR 10 and CHARMM 9 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 for coordinate velocity force or other data being read or written by NAMD This is the standard format for coordina
215. mulation 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 96 e SMDk2 lt force constant for transverse direction to use in SMD simulation gt Acceptable Values positive real Default Value 0 Description SMD transverse harmonic constraint force constant Must be specified in kcal mol A The conversion factor is 1 kcal mol 69 479 pN A e SMDVel lt Velocity of the SMD reference position movement gt Acceptable Values nonzero real timestep Description The velocity of the SMD center of mass movement Gives the absolute value e SMDDir lt Direction of the SMD center of mass movement gt Acceptable Values non zero vector Description The direction of the SMD reference position movement The vector does not have to be normalized it is normalized by NAMD before being used e SMDOutputFreq lt frequency of SMD output gt Acceptable Values positive integer Default Value 1 Description The frequency in timesteps with which the current SMD data values are printed out 9 9 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 Value
216. n Like atomsCol for atomsFile indicates which column to use to identify the atoms in refPositionsFile If not specified atoms are selected by index based on the atom group definition e refPositionsColValue lt atom group Value in the PDB column gt Acceptable Values positive decimal Description Analogous to atomsColValue but applied to refPositionsCol e refPositionsGroup lt atom group Use an alternate group do perform roto translational fitting gt Acceptable Values Block refPositionsGroup Default Value This group itself Description If either centerReference or rotateReference is defined this keyword allows to define an additional atom group which is used instead of the current one to calculate the translation or the rotation to the reference positions For example it is possible to use all the backbone heavy atoms of a protein to set the reference frame but only involve a more localized group in the colvar s definition e disableForces lt atom group Don t apply colvar forces to this group gt Acceptable Values boolean Default Value off Description If this option is on all the forces applied from the colvars to the atoms in this group are ignored The applied forces on each colvar are still written to the trajectory file if requested In some cases it may be desirable to use this option in order not to perturb the motion of certain atoms Note when used the biasing forces are not applied uniformly a non
217. n Angstroms between the the centers of mass of the ligand and the protein when the simulation is stopped ramd firstProtAtom lt First index of protein atom gt Acceptable Values positive integer Default Value 1 Description Specifies the index of the first protein atom ramd lastProtAtom lt Last index of protein atom gt Acceptable Values positive atom Description Specifies the index of the last protein atom ramd firstRamdAtom lt First index of ligand atom gt Acceptable Values positive integer Description Specifies the index of the first ligand atom 163 e ramd lastRamdAtom lt Last index of ligand atom gt Acceptable Values positive integer Description Specifies the index of the last ligand atom e ramd ramdSeed lt Set RAMD seed gt Acceptable Values positive integer Default Value 14253 Description Specifies seed for the random number generator for generation of acceleration directions Change this parameter if you wish to run different trajectories with identical parameters Note In combined RAMD MD simulations RAMD blocks alternate with standard MD blocks ramdSteps and mdSteps input parameters The switches between RAMD and MD blocks are decided based on the following parameters i d the distance between the protein and ligand centers of mass ii dr the distance traveled by the ligand in 1 RAMD block and iii dm the distance traveled by the ligand in 1 MD block A
218. n defined as N RMSD O 4 JU Gilt xeog t EI i 1 The optimal rotation U Gao is calculated within the formalism developed in reference 16 a ref which guarantees a continuous dependence of UP u Wi kx 7 with respect to x t The options for rmsd are e atoms lt rmsd Atom group gt Acceptable Values atoms block Description Defines the group of atoms of which the RMSD should be calculated 120 e refPositions lt rmsd Reference coordinates gt Acceptable Values space separated list of x y z triplets Description This option mutually exclusive with refPositionsFile sets the reference coordinates to be compared with The list should be as long as the atom group atoms This option is independent from that with the same keyword within the atoms block e refPositionsFile lt rmsd Reference coordinates file gt Acceptable Values UNIX filename Description This option mutually exclusive with refPositions sets the PDB file name for the reference coordinates to be compared with The format is the same as that provided by refPositionsFile within an atom group definition but the two options function inde pendently Note that as a rule rotateReference and associated keywords should NOT be used within the atom group atoms of an rmsd component e refPositionsCol lt rmsd PDB column to use gt Acceptable Values X Y Z 0 or B Description If refPositionsFile is define
219. n this Agreement 5 By using or copying this Software Licensee agrees to abide by the copyright law and all other applicable laws of the U S including but not limited to export control laws and the terms of this license Illinois shall have the right to terminate this license immediately by written notice upon Licensee s breach of or non compliance with any of its terms Licensee may be held legally responsible for any copyright infringement that is caused or encouraged by its failure to abide by the terms of this license Upon termination Licensee agrees to destroy all copies of the Software in its possession and to verify such destruction in writing 6 The user agrees that any reports or published results obtained with the Software will ac knowledge its use by the appropriate citation as follows NAMD was developed by the Theoretical 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 publicat
220. n two reference groups e main lt distanceZ distanceXY Main group of atoms gt Acceptable Values Block main Description Group of atoms whose position r is measured e ref lt distanceZ distanceXY Reference group of atoms gt Acceptable Values Block ref Description Reference group of atoms The position of its center of mass is noted r below e ref2 lt distanceZ distanceXY Secondary reference group gt Acceptable Values Block ref2 Default Value none Description Optional group of reference atoms whose position ra can be used to define a dynamic projection axis e rz2 ri x r2 r In this case the origin is rm 1 2 r1 r2 and the value of the component is e r rm e axis lt distanceZ distanceXY Projection axis A gt Acceptable Values x y z triplet Default Value 0 0 0 0 1 0 Description The three components of this vector define when normalized a projection axis e for the distance vector r r joining the centers of groups ref and main The value 117 of the component is then e r r1 The vector should be written as three components separated by commas and enclosed in parentheses e forceNoPBC lt distanceZ distanceXY Calculate absolute rather than minimum image distance gt Acceptable Values boolean Default Value no Description This parameter has the same meaning as that described above for the distance component e oneS
221. namic cycle perturbation of intramolecular terms may by and large be safely avoided 8 This property is controlled by the alchDecouple keyword described in 11 1 2 Free Energy Perturbation Within the FEP framework 6 13 14 23 37 44 63 66 70 the free energy difference between two alternate states a and b is expressed by 144 AA gt In exp 8 Po x Pr Hal Px 56 Here 87 kgT where kg is the Boltzmann constant T is the temperature Ha x pz2 and Hp x Pz are the Hamiltonians describing states a and b respectively denotes an ensemble average over configurations representative of the initial reference state a a e X a X b X c Figure 8 Convergence of an FEP calculation If the ensembles representative of states a and b are too disparate equation 56 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 Px is assumed to be identical for state a and state b Convergence of equation 56 implies that low energy configurations of the target state b are also configurations of the reference state
222. nate e selectConstrX lt Restrain X components of coordinates gt Acceptable Values on or off Default Value off Description Restrain the Cartesian x components of the positions e selectConstrY lt Restrain Y components of coordinates gt Acceptable Values on or off Default Value off Description Restrain the Cartesian y components of the positions e selectConstrZ lt Restrain Z components of coordinates gt Acceptable Values on or off Default Value off Description Restrain the Cartesian z components of the positions 5 6 3 Fixed atoms parameters Atoms may be held fixed during a simulation NAMD avoids calculating most interactions in which all affected atoms are fixed unless fixedAtomsForces is specified e fixedAtoms lt are there fixed atoms gt Acceptable Values on or off Default Value off Description Specifies whether or not fixed atoms are present e fixedAtomsForces lt are forces between fixed atoms calculated gt Acceptable Values on or off Default Value off Description Specifies whether or not forces between fixed atoms are calculated This option is required to turn fixed atoms off in the middle of a simulation These forces will affect the pressure calculation and you should leave this option off when using constant pressure if the coordinates of the fixed atoms have not been minimized The use of constant pressure with significant numbers of fixed atoms is not recommended e fixedAtomsFile
223. ncWithColvar lt colvar Colvar name for the correlation function gt Acceptable Values string Description By default the auto correlation function ACF of this colvar amp is cal culated When this option is specified the correlation function is calculated instead with another colvar which must be of the same type scalar vector or quaternion as e corrFuncType lt colvar Type of the correlation function gt Acceptable Values velocity coordinate or coordinate_p2 Default Value velocity Description With coordinate or velocity the correlation function C t II amp to to t is calculated between the variables and or their velocities II amp is the scalar product when calculated between scalar or vector values whereas for quater nions it is the cosine between the two corresponding rotation axes With coordinate_p2 the second order Legendre polynomial 3 cos 1 2 is used instead of the cosine e corrFuncNormalize lt colvar Normalize the time correlation function gt Acceptable Values boolean Default Value on Description If enabled the value of the correlation function at t 0 is normalized to 1 otherwise it equals to O amp amp 129 e corrFuncLength lt colvar Length of the time correlation function gt Acceptable Values positive integer Default Value 1000 Description Length in number of points of the time correlation function e cor
224. nd force between these groups for each frame in the DCD file It is assumed that coordinate frames were written every 1000 timesteps See Sec 14 1 for more about pair interaction calculations initial config coordinates alanin pdb temperature 0 output params outputname tmp alanin analyze binaryoutput no integrator params timestep 1 0 force field params structure alanin psf parameters alanin params exclude scaled1 4 1 4scaling 1 0 switching on switchdist 8 0 cutoff 12 0 pairlistdist 13 5 stepspercycle 20 Atoms in group 1 have a 1 in the B column group 2 has a 2 pairInteraction on pairInteractionFile pair pdb pairInteractionCol B pairInteractionGroup1 1 pairInteractionGroup2 2 First frame saved was frame 1000 set ts 1000 coorfile open dcd tmp alanin dcd Read all frames until nonzero is returned while coorfile read 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 0 178 incr ts 1000 coorfile close 179 17 Running NAMD NAMD runs on a variety of serial and parallel platforms While it is trivial to launch a serial program a parallel program depends on a platform specific library such as MPI to launch copies of itself on other nodes and to provide access to a high performance network such as Myrinet or InfiniBand if one is available For typical workstations Window
225. nd P A Kollman Use of locally enhanced sampling in free energy calculations Testing and application to the a 8 anomerization of glucose J Am Chem Soc 120 23 5771 5782 1998 C Simmerling M R Lee A R Ortiz A Kolinski J Skolnick and P A Kollman Com bining MONSSTER and LES PME to predict protein structure from amino acid sequence Application to the small protein CMTI 1 J Am Chem Soc 122 35 8392 8402 2000 R D Skeel and J J Biesiadecki Symplectic integration with variable stepsize Ann Numer Math 1 191 198 1994 J Srinivasan M W Trevathan P Beroza and D A Case Application of a pairwise gen eralized born model to proteins and nucleic acids inclusion of salt effects Theor Chem Acc 101 426 434 1999 W C Still A Tempczyk R C Hawley and T Hendrickson Semianalytical treatment of solvation for molecular mechanics and dynamics J Am Chem Soc 112 6127 6129 1990 T P Straatsma and J A McCammon Multiconfiguration thermodynamic integration J Chem Phys 95 1175 1118 1991 193 63 64 65 66 67 68 69 70 T P Straatsma and J A McCammon Computational alchemy Annu Rev Phys Chem 43 407 435 1992 B T Thole Molecular polarizabilities calculated with a modified dipole interaction Chem Phys 59 341 350 1981 P Van Duijnen and M Swart Molecular and atomic polarizabilities Thole s model revisited J Phys Chem A 102
226. ng 0 false 1 e h increment for the history dependent bias hill height 0 01 kcal mol e f if non zero this factor is used to scale the increment stepwise in the second half of the M C sampling to refine the free energy estimate 0 5 Using the default values of all parameters should give reasonable results in most cases abf_integrate produces the following output files e lt gradient file gt pmf computed free energy surface e lt gradient file gt histo histogram of M C sampling not usable in a straightforward way if the history dependent bias has been applied e lt gradient_file gt est estimated gradient of the calculated free energy surface from finite differences e lt gradient_file gt dev deviation between the user provided numerical gradient and the ac tual gradient of the calculated free energy surface The RMS norm of this vector field is used as a convergence criteria and displayed periodically during the integration Note Typically the deviation vector field does not vanish as the integration converges This happens because the numerical estimate of the gradient does not exactly derive from a potential due to numerical approximations used to obtain it finite sampling and discretization on a grid 10 3 2 Metadynamics Many methods have been introduced in the past that make use of an artificial energy term that changes and adapts over time to reconstruct a potential of mean force fro
227. nit vector vector or quaternion By default the colvar is the sum of its components Linear or polynomial combinations following equation 36 can be obtained by setting the following parameters which are common to all components e componentCoeff lt any component Coefficient of this component in the colvar gt Acceptable Values decimal Default Value 1 0 Description Defines the coefficient by which this component is multiplied after being raised to componentExp before being added to the sum e componentExp lt any component Exponent of this component in the colvar gt Acceptable Values integer Default Value 1 Description Defines the power at which the value of this component is raised before being added to the sum When this exponent is different than 1 non linear sum system forces and the Jacobian force are not available making the colvar unsuitable for ABF calculations Example To define the average of a colvar across different parts of the system simply define within the same colvar block a series of components of the same type applied to different atom groups and assign to each component a componentCoeff of 1 N 10 2 4 Defining atom groups Each component depends on one or more atom groups which can be defined by different methods in the configuration file Each atom group block is initiated by the name of the group itself within the component block followed by the instructions to the colvar module on how to
228. njugate gradient and line search algorithm with much better performance than the older velocity quenching method The method of conjugate gradients 68 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 minimizer gt Acceptable Values positive decimal Default Value 1 0e 4 Description Varying this might improve conjugate gradient performance 7 2 2 Velocity quenching parameters You can perform energy minimization using a simple quenching scheme While this algorithm is not the mo
229. nly when a simulation is a continuation of a previous simulation In this case rather than having the timestep restart at 0 a specific timestep number can be specified 7 3 2 Initialization e temperature lt initial temperature K gt Acceptable Values positive decimal Description Initial temperature value for the system Using this option will generate a random velocity distribution for the initial velocities for all the atoms such that the system is at the desired temperature Either the temperature or the velocities binvelocities option must be defined to determine an initial set of velocities Both options cannot be used together e COMmotion lt allow initial center of mass motion gt Acceptable Values yes or no Default Value no Description Specifies whether or not motion of the center of mass of the entire system is allowed If this option is set to no the initial velocities of the system will be adjusted to remove center of mass motion of the system Note that this does not preclude later center of mass motion due to external forces such as random noise in Langevin dynamics boundary potentials and harmonic restraints e seed lt random number seed gt Acceptable Values positive integer Default 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 sa
230. ns and aliases If no arguments are provided the current context is returned If lt context gt or new is specified a new context is entered and the old context is returned If delete is also specified the old context is destroyed and deleted lt old context gt is returned An error is returned if the specified context does not exist or if delete was specified and the current context would still be in use It may be possible to write robust error tolerant code with this interface but it would not be easy Please employ the following revised psfcontext usage instead Arguments lt contert gt Context ID returned by psfcontext Context At any time psfcontext mixedcase Purpose Make context case sensitive by preserving case of all segment residue atom and patch names on input Arguments Context Before reading files requiring case sensitive behavior normally as the first com mand psfcontext allcaps Purpose Make context case insensitive by converting all segment residue atom and patch names to upper case characters on input This is the default behavior and should match the behavior of versions prior to 1 5 0 Arguments Context Before reading files requiring case insensitive behavior not needed in normal use psfcontext reset Purpose Clears the structure topology definitions and aliases creating clean environment just like a new context Arguments Context At any time psfcontext create Purpose Cr
231. nt ka controls the potential perpendicular to Output NAMD provides output of the current SMD data The frequency of output is specified by the SMDOutputFreq parameter in the configuration file Every SMDOutputFreq timesteps NAMD will print the current timestep current position of the center of mass of the restrained atoms and the current force applied to the center of mass in piconewtons pN The output line starts with word SMD Parameters The following parameters describe the parameters for the SMD feature of NAMD e SMD lt Are SMD features active gt Acceptable Values on or off Default Value off Description Should SMD harmonic constraint be applied to the system If set to on then SMDk SMDFile SMDVel and SMDDir must be defined Specifying SMDOutputFreq is optional e SMDFile lt SMD constraint reference position gt Acceptable Values UNIX filename Description File to use for the initial reference position for the SMD harmonic constraints All atoms in this PDB file with a nonzero value in the occupancy column will be tagged as SMD atoms The coordinates of the tagged SMD atoms will be used to calculate the initial center of mass During the simulation this center of mass will move with velocity SMDVel in the direction SMDDir The actual atom order in this PDB file must match that in the structure or coordinate file since the atom number field in this PDB file will be ignored e SMDk lt force constant to use in SMD si
232. nto two pieces a quickly varying local component and a slower long range component The local force component is defined in terms of a splitting function The local force component consists of all bonded and van der Waals interactions as well as that portion of electrostatic interactions for pairs that are separated by less than the local interaction distance determined by the splitting function The long range component consists only of electrostatic interactions outside of the local interaction distance Since the long range forces are slowly varying they are not evaluated every timestep Instead they are evaluated every k timesteps specified by the NAMD parameter fullElectFrequency An impulse of k times the long range force is applied to the system every k timesteps i e the r RESPA integrator is used For appropriate values of k it is believed that the error introduced by this infrequent evaluation is modest compared to the error already incurred by the use of the numerical Verlet integrator Improved methods for incorporating these long range forces are currently being investigated with the intention of improving accuracy as well as reducing the frequency of long range force evaluations In the scheme described 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
233. number of LES images to use gt Acceptable Values positive integer equal to the number of images present Description This should be equal to the factor used in multiply when creating the structure The interaction potentials for images is divided by lesFactor e lesReduceTemp lt reduce enhanced atom temperature gt Acceptable Values on or off Default Value off Description Enhanced atoms experience interaction potentials divided by lesFactor This allows them to enter regions that would not normally be thermally accessible If this is not desired then the temperature of these atoms may 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 158 this option since in a constant energy simulation energy will flow into the enhanced degrees of freedom until they reach thermal equilibrium with the rest of the system The reduced temperature atoms will have reduced velocities as well unless lesReduceMass is also enabled e lesReduceMass lt reduce enhanced atom mass gt Acceptable Values on or off Default Value off Description Used with lesReduceTemp to restore velocity distribution to enhanced atoms If used alone enhanced atoms would move faster than normal atoms and hence a smaller timestep would be required e lesFile lt PDB file containing LES flags gt Acce
234. obably 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 e pairlistdist lt distance between pairs for inclusion in pair lists A gt Acceptable Values positive decimal gt cutoff Default Value cutoff Description A pair list is generated pairlistsPerCycle times each cycle containing pairs of atoms for which electrostatics and van der Waals interactions will be calculated This parameter is used when switching is set to on to specify the allowable distance between atoms for inclusion in the pair list This parameter is equivalent to the X PLOR parameter 82 CUTNb If no atom moves more than pairlistdist cutoff during one cycle then there will be no jump in electrostatic or van der Waals energies when the next pair list is built Since such a jump is unavoidable when truncation is used this parameter may only be specified when switching is set to on If this parameter is not specified and switching is set to on the value of cutoff is used A value of at least one greater than cutoff is recommended stepspercycle lt timesteps per cycle gt Acceptable Values positive integer Default Value 20 Description Number of timesteps in each cycle Each cycle repres
235. of an exnihilated or appearing particle are linearly coupled to the simulation over the A value range of alchElecLambdaStart 1 0 At A values less than or equal to the user defined value of alchElecLambdaStart electrostatic interactions of the exnihilated particle are fully decoupled from the simulation Coupling of electrostatic interactions then increases linearly for increasing values of A until A 1 0 at which point electrostatic interactions of the exnihilated particle are fully coupled to the simulation For annihilated or vanishing particles the electrostatic interactions are linearly decoupled from the simulation over the A value range of 0 1 0 alchElecLambdaStart At A 0 electrostatic interactions are fully coupled to the simulation and then linearly decreased with increasing A such that at A values greater than or equal to 1 0 alchElecLambdaStart electrostatic interactions are completely decoupled from the simulation Two examples shown in Figure 9 describe the relationship between the user defined value of A and the coupling of electrostatic or vdW interactions to the simulation e alchVdwLambdaEnd lt Value of A to cancel van der Waals interactions gt Acceptable Values positive decimal Default Value 1 0 Description If the alchElecLambdaStart option is used it may also be desirable to separate the scaling of van der Waals and electrostatic interactions alchVdwLambdaEnd sets the value of A above which all vdW in
236. ollyIterations parameter 73 mollyTolerance parameter 73 movingConstraints parameter 90 movingConsVel parameter 90 MTSAlgorithm parameter 72 multipleReplicas parameter 137 multiply psfgen command 37 mutate psfgen command 37 name parameter 111 130 139 newHillFrequency parameter 137 nonbondedFreq parameter 72 nonbondedScaling parameter 16 46 numNodes command 16 numPes command 16 numPhysicalNodes command 16 numsteps parameter 69 oneSiteSystemForce parameter 117 119 OPLS 47 output command 15 output onlyforces command 15 output withforces command 15 outputAppliedForce parameter 113 outputEnergies parameter 23 outputEnergy parameter 113 outputFreq parameter 133 142 outputMomenta parameter 23 outputname parameter 20 outputPairlists parameter 84 outputPressure parameter 23 outputSystemForce parameter 113 outputTiming parameter 23 output Value parameter 112 outputVelocity parameter 112 pairInteraction parameter 168 pairInteractionCol parameter 168 198 pairInteractionFile parameter 168 pairInteractionGroupl parameter 168 pairInteractionGroup2 parameter 168 pairInteractionSelf parameter 168 pairlistdist parameter 82 pairlistGrow parameter 84 pairlistMinProcs parameter 83 pairlistShrink parameter 84 pairlistsPerCycle parameter 83 pairlist Trigger parameter 84 parameters parameter 19 para TypeCharmm parameter 19 para TypeXplor parameter 19 parmfile parameter 24 patch psfgen c
237. ommand 37 pdb psfgen command 36 pdbalias atom psfgen command 39 pdbalias residue psfgen command 35 period parameter 115 PME parameter 47 PMEGridSizeX parameter 48 PMEGridSizeY parameter 48 PMEGridSizeZ parameter 48 PMEGridSpacing parameter 48 PMEInterpOrder parameter 47 PMEProcessors parameter 48 PMETolerance parameter 47 PRESSAVG 23 pressureProfile parameter 169 pressureProfileAtomTypes parameter 170 pressureProfileAtomTypesCol parameter 171 pressureProfileAtomTypesFile parameter 171 pressureProfileEwald parameter 170 pressureProfileEwaldX parameter 170 pressureProfileEwaldY parameter 170 pressureProfileEwaldZ parameter 170 pressureProfileFreq parameter 170 pressureProfileSlabs parameter 169 print command 15 psfcontext allcaps psfgen command 38 psfcontext create psfgen command 38 psfcontext delete psfgen command 38 psfcontext eval psfgen command 39 psfcontext mixedcase psfgen command 38 psfcontext psfgen command 38 psfcontext reset psfgen command 38 psfcontext stats psfgen command 39 psfSegID parameter 123 126 ramd accel parameter 163 ramd debugLevel parameter 162 ramd firstProtAtom parameter 163 ramd firstRamdAtom parameter 163 ramd forceOutFreq parameter 163 ramd lastProtAtom parameter 163 ramd lastRamdAtom parameter 164 ramd maxDist parameter 163 ramd mdStart parameter 162 ramd mdSteps parameter 162 ramd ramdSeed parameter 164 ramd ramdSteps parameter 162 ramd rMinMd par
238. on straints The reference positions of all constrained atoms are then rotated with a given angular 90 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 will move all reference positions Only one of the moving and rotating constraints can be used at a time Using very soft
239. on Between the two equivalent quaternions q0 q1 42 q3 and qo q1 G2 q3 the closer to 1 0 0 0 0 0 0 0 is chosen This simplifies 122 the visualization of the colvar trajectory when samples values are a smaller subset of all possible rotations Note this only affects the output never the dynamics Hint stopping the rotation of a protein To stop the rotation of an elongated macro molecule in solution and use an anisotropic box to save water molecules it is possible to define a colvar with an orientation component and restrain it throuh the harmonic bias around the identity rotation 1 0 0 0 0 0 0 0 Only the overall orientation of the macromolecule is affected and not its internal degrees of freedom The user should also take care that the macro molecule is composed by a single chain or disable wrapA11 otherwise Component orientationAngle angle of rotation from reference coordinates The block orientationAngle accepts the same options as rmsd and orientation atoms refPositions refPositionsFile and refPositionsCol but it returns instead the angle of rotation w between the current and the reference positions This angle is expressed in degrees within the range 0 180 Component alpha a helix content of a protein segment The block alpha defines the parameters to calculate the helical content of a segment of protein residues The a helical content across the N 1 residues No to No N
240. on EXPERIMENTAL ExcludeFromPressureFile lt File specifying excluded atoms gt Acceptable Values PDB file Default Value coordinates file Description PDB file with one column specifying which atoms to exclude from pressure rescaling Specify 1 for excluded and 0 for not excluded ExcludeFromPressureCol lt Column in PDB file for specifying excluded atoms gt Acceptable Values O B X Y or Z Default Value O Description Specifies which column of the pdb file to check for excluded atoms 80 8 Performance Tuning 8 1 Non bonded interaction distance testing The last critical parameter for non bonded interaction calculations is the parameter pairlistdist To reduce the cost of performing the non bonded interactions NAMD uses a non bonded pair list which contained all pairs of atoms for which non bonded interactions should be calculated Per forming the search for pairs of atoms that should have their interactions calculated is an expensive operation Thus the pair list is only calculated periodically at least once per cycle Unfortunately pairs of atoms move relative to each other during the steps between preparation of the pair list Because of this if the pair list were built to include only those pairs of atoms that are within the cutoff distance when the list is generated it would be possible for atoms to drift closer to gether than the cutoff distance during subsequent timesteps and yet not have their non bonded intera
241. on thread into a single process Since one core per process is used for the communication thread SMP builds are typically slower than non SMP builds The advantage of SMP builds is that many data structures are shared among the threads reducing the per core memory footprint when scaling large simulations to large numbers of cores SMP builds launched with charmrun use p to specify the total number of PEs worker threads and ppn to specify the number of PEs per process Thus to run one process with one communi cation and three worker threads on each of four quad core nodes one would specify 182 charmrun namd2 p12 ppn 3 lt configfile gt For MPI based SMP builds one would specify any mpiexec options needed for the required number of processes and pass ppn to the NAMD binary as mpiexec np 4 namd2 ppn 3 lt configfile gt See the Cray XT directions below for a more complex example 17 6 Cray XT You will need to load the GNU compiler module build Charm for mpi crayxt and NAMD for CRAY XT g use the following command in your batch script aprun n PBS_NNODES cc cpu namd2 To reduce memory usage build Charm mpi crayxt smp instead and use assuming you have 12 cores per node on your machine setenv MPICH_PTL_UNEX_EVENTS 100000 NPROC PBS_NNODES 12 aprun n NPROC N 1 d 12 namd2 ppn 11 setcpuaffinity pemap 1 11 commap 0 For two processes per node for possibly better scaling use setenv MPICH_PTL_UN
242. on scalar a final restriction can arise when calculating system force outputSystemForce option or application of a abf bias System forces are available currently only for the following components distance distanceZ distanceXY angle dihedral rmsd eigenvector and gyration Syntax of a component definition Most components make use of one or more atom groups whose syntax of definition is by their name followed by a definition block like atoms or group1 and group2 The contents of an atom group block are described in 10 2 4 In the following all the available component types are listed along with their physical units and the limiting values if any Such limiting values can be used to define lowerBoundary and upperBoundary in the parent colvar Component distance center of mass distance between two groups The distance block defines a distance component between two atom groups group1 and group2 e groupl lt distance First group of atoms gt Acceptable Values Block group1 Description First group of atoms e group2 lt distance Second group of atoms gt Acceptable Values Block group2 Description Second group of atoms 116 e forceNoPBC lt distance Calculate absolute rather than minimum image distance gt Acceptable Values boolean Default Value no Description By default in calculations with periodic boundary conditions the distance component returns the distance accordin
243. onds is all waters are made rigid as described above and the bond between each hydrogen and the one atom to which it is bonded is similarly constrained For the default case none no lengths are constrained e rigidTolerance lt allowable bond length error for ShakeH A gt Acceptable Values positive decimal Default Value 1 0e 8 Description The ShakeH algorithm is assumed to have converged when all constrained bonds differ from the nominal bond length by less than this amount e rigidlterations 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 e 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 54 useSettle lt Use SETTLE for waters gt Acceptable Values on or off Default Value on Description If rigidBonds are enabled then use the non iterative SETTLE algorithm to keep waters rigid rather than the slower SHAKE algorithm 5 6 2 Harmonic restraint parameters The following describes the parameters
244. onstrX parameter 56 selectConstr Y parameter 56 selectConstrZ parameter 56 SMD parameter 96 SMDDir parameter 97 SMDFile parameter 96 SMDk parameter 96 SMDk2 parameter 97 SMDOutputFreq parameter 97 SMDVel parameter 97 solventDielectric parameter 63 source command 15 sphericalBC parameter 66 sphericalBCCenter parameter 66 sphericalBCexp1 parameter 67 sphericalBCexp2 parameter 67 sphericalBCk1 parameter 66 sphericalBCk2 parameter 67 sphericalBCrl1 parameter 66 sphericalBCr2 parameter 67 splitPatch parameter 83 stepspercycle parameter 83 StrainRate parameter 80 structure parameter 19 surfaceTension parameter 64 SurfaceTensionTarget parameter 15 80 switchdist parameter 46 switching parameter 45 symmetryFile parameter 92 symmetryFirstFullStep parameter 92 symmetryFirstStep parameter 93 symmetryk parameter 92 symmetrykFile parameter 92 symmetryLastFullStep parameter 92 symmetryLastStep parameter 93 symmetryMatrixFile parameter 93 symmetryRestraints parameter 92 symmetryScaleForces parameter 92 tableInterpType parameter 50 tabulatedEnergies parameter 50 tabulatedEnergiesFile parameter 50 targetCenters parameter 140 targetEquilSteps parameter 141 targetForceConstant parameter 140 targetForceExponent parameter 141 targetNumStages parameter 141 targetNumSteps parameter 141 tclBC parameter 101 tclBCArgs parameter 102 tclBCScript parameter 101 tclForces parameter 98 tclForces
245. or the collective variables gt Acceptable Values UNIX filename Description This file contains the definition of all collective variables and their biasing or analysis methods It is meant to contain all the information needed to begin a colvars simulation Additional information is needed instead to continue a previous run which is read from the file provided by colvarsInput Parameters within the configuration file can be controlled from a NAMD config file using Tcl variables in the following way colvars on colvarsConfig colvars_subst tmp set myParameter someValue Parse template and create specific config file on the fly set infile open colvars_template in r 107 set outfile open colvars_subst tmp wt puts outfile subst read infile close infile close outfile In this example the string myParameter will be replaced with the value someValue wherever it appears in the file colvars_template in This value will then be read in by the colvars module when it parses its input e colvarsInput lt Input state file for the collective variables gt Acceptable Values UNIX filename Description When continuing a previous simulation run this file contains the current state of all collective variables and their biasing methods Its format is similar to that of colvarsConfig but with different keywords In normal circumstances this file is written automatically at the end of a NAMD run and the user does not need to edit it
246. otential Note that cannot be set to zero otherwise the derivative of the modified potential is discontinuous From an aMD simulation the ensemble average 4 of an observable A r can be calculated using the following reweighting procedure A r exp BAV 1 exp BAV 1 in which G 1 kgT and and represent the ensemble average in the original and the aMD ensembles respectively Currently aMD can be applied in three modes in NAMD aMDd aMDT and aMDdual 68 The boost energy is applied to the dihedral potential in the aMDd mode the default mode and to the total potential in the aMDT mode In the dual boost mode aMDdual 25 two independent boost energies are applied one on the dihedral potential and the other on the Total Dihedral 4 62 potential 153 Figure 11 Schematics of the aMD method When the original potential thick line falls below a threshold energy E dashed line a boost potential is added The modified energy profiles thin lines have smaller barriers separating adjacent energy basins 12 1 2 NAMD parameters The following parameters are used to enable accelerated MD e accelMD lt Is accelerated molecular dynamics active gt Acceptable Values on or off Default Value off Description Specifies if accelerated MD is active e accelMDdihe lt Apply boost to dihedrals gt Acceptable Values on or off Default Value on Description Only ap
247. otes an absence of interaction the interatomic distances used in the Lennard Jones potential are shifted according to 5 43 r r alchVdWShiftCoeff x 1 2 alchElecLambdaStart lt Value of to introduce electrostatic interactions gt Acceptable Values positive decimal Default Value 0 5 Description In order to avoid the so called end point catastrophes it is crucial to avoid situations where growing particles overlap with existing particles with an unbounded interaction potential which would approach infinity as the interaction distance approaches zero 5 14 One possible route for avoiding overlap of unbounded electrostatic poten tials consists of allowing a bounded soft core vdW potential using a positive value of alchVdWShiftCoeff to repel first all overlapping particles at low values of A As A increases once the particles are repelled it becomes safe to turn on FEP or TI electrostatics 147 Decoupling Mutation elecLambdaStart 0 5 vdwLambdaEnd 1 0 elecLambdaStart 0 5 vdwLambdaEnd 0 7 ale o LEF o 2 2 w F Ss gt gt 0 4 A 0 2 0 fe esl Se 0 E 3 0 02 04 06 08 1 0 02 04 06 08 1 A user controlled A user controlled Figure 9 Relationship of user defined A to coupling of electrostatic or vdW interactions to a simulation given specific values of alchElecLambdaStart or alchVdwLambdaEnd In the current implementation the electrostatic interactions
248. oup of atoms that do not change during the simulation e g the environment ii the atoms describing the reference state a of the system and iii the atoms that correspond to the target state b at the end of the alchemical transformation The atoms representative of state a should never interact with those of state b throughout the MD simulation Such a setup in which atoms of both the initial and the final states of the system are present in the molecular topology file i e the psf file is characteristic of the so called dual topology paradigm 22 51 2 The hybrid Hamiltonian of the system is a function of the general extent parameter A which connects smoothly state a to state b In the simplest case such a connection may be achieved by linear combination of the corresponding Hamiltonians H X Pz A Ho x px AHy x Px 1 A Ha x Pz 54 where Ha x Pz describes the interaction of the group of atoms representative of the reference state a with the rest of the system Hj x Px characterizes the interaction of the target topology b with the rest of the system Ho x p is the Hamiltonian describing those atoms that do not undergo any transformation during the MD simulation For instance in the point mutation of an alanine side chain into that of glycine by means of a free energy calculation either free energy perturbation or thermodynamic integration the topology of both the methyl group of alanine
249. owed Tcl commands and variables are not available if a keyword requiring a boolean value yes on true or no off false is provided without an explicit value it defaults to yes on true for example outputAppliedForce may be used as shorthand for outputAppliedForce on Three global options are available colvarsTrajFrequency lt global Colvar value trajectory frequency gt Acceptable Values positive integer Default Value 100 Description The values of each colvar and any additional quantities which have been set to be reported are written at this frequency to the file lt outputName gt colvars traj If the value is 0 the trajectory file is not written For optimization the output is buffered as is the NAMD log output in most operating systems but it is synchronized with the disks every time the restart file is written colvarsTrajAppend lt global Append to trajectory file gt Acceptable Values boolean Default Value off Description If this flag is enabled and a file with the same name as the trajectory file is already present new data is appended to that file Otherwise a new file is created Note when running consecutive simulations with the same outputName e g in FEP calculations you should enable this option to preserve the previous contents of the trajectory file colvarsRestartFrequency lt global Colvar module restart frequency gt Acceptable Values positive integer Default
250. parameter 68 cylindricalBCk1 parameter 68 cylindricalBCk2 parameter 68 cylindricalBCll parameter 68 cylindricalBCl2 parameter 68 cylindricalBCr1 parameter 68 cylindricalBCr2 parameter 68 DCDfile parameter 21 DCDfreq parameter 22 DCDUnitCell parameter 22 delatom psfgen command 37 196 dielectric parameter 46 disableForces parameter 128 drude parameter 52 drudeBondConst parameter 53 drudeBondLen parameter 53 drudeDamping parameter 53 drudeNbTholeCut parameter 53 drudeTemp parameter 53 dummyAtom parameter 127 dumpFreeEnergyFile parameter 137 dumpPartialFreeEnergyFile parameter 138 eField parameter 16 85 eFieldFreq parameter 16 eFieldOn parameter 85 eFieldPhase parameter 16 error message Atoms moving too fast 82 Bad global exclusion count 82 exclude parameter 46 ExcludeFromPressure parameter 80 ExcludeFromPressureCol parameter 80 ExcludeFromPressureFile parameter 80 exit command 16 expandBoundaries parameter 112 expDenom parameter 119 expNumer parameter 119 extCoordFilename parameter 104 extendedFluctuation parameter 113 extendedLagrangian parameter 113 extendedLangevinDamping parameter 114 extendedSystem parameter 65 extendedTemp parameter 114 extended TimeConstant parameter 114 extForceFilename parameter 104 extForces parameter 104 extForcesCommand parameter 104 extraBonds parameter 57 extraBondsFile parameter 57 FFTWEstimate parameter 48 FFTWUseWisdom parameter 48
251. plies boost to the dihedral potential By default accelMDdihe is turned on and the boost energy is applied to the dihedral potential of the simulated system When accelMDdihe is turned off aMD switches to the accelMDT mode and the boost is applied to the total potential e accelMDE lt Threshold energy E gt Acceptable Values Real number Description Specifies the threshold energy E in the aMD equations e accelMDalpha lt Acceleration factor a gt Acceptable Values Positive real number Description Specifies the acceleration factor a in the aMD equations e accelMDdual lt Use dual boost mode gt Acceptable Values on or off Default Value off Description When accelMDdual is on aMD switches to the dual boost mode Two inde pendent boost potentials will be applied one to the dihedral potential that is controlled by 154 the parameters accelMDE and accelMDalpha and a second to the Total Dihedral potential that is controlled by the accelMDTE and accelMDTalpha parameters described below accelMDTE lt Threshold energy F in the dual boost mode gt Acceptable Values Real number Description Specifies the threshold energy E used in the calculation of boost energy for the Total Dihedral potential This option is only available when accelMDdual is turned on accelMDTalpha lt Acceleration factor a in the dual boost mode gt Acceptable Values Positive real number Description Specifies the acceleration factor a u
252. pply a patch to one or more residues Patches make small modifications to the structure of residues such as converting one to a terminus changing the protonation state or creating disulphide bonds between a pair of residues Arguments list Lists all patches applied explicitey using the command patch listall Lists all currently applied patches including default patches lt patch residue name gt Name of patch residue from topology definition file lt segid resid gt List of segment and residue pairs to which patch should be applied Context After one or more segments have been built regenerate angles dihedrals Purpose Remove all angles and or dihedrals and completely regenerate them using the segment automatic generation algorithms This is only needed if patches were applied that do not correct angles and bonds Segment and file defaults are ignored and angles dihedrals for the entire molecule are 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
253. ps between the generation of restart files NAMD Parameter DCDfile X PLOR Parameter TRAJectory Filename for the position trajectory file NAMD Parameter DCDfreq X PLOR Parameter NSAVC Number of timesteps between writing coordinates to the trajectory file NAMD Parameter velDCDfile X PLOR Parameter VELOcity Filename for the velocity trajectory file NAMD Parameter velDCDfreq X PLOR Parameter NSAVV Number of timesteps between writing velocities to the trajectory file NAMD Parameter numsteps X PLOR Parameter NSTEp Number of simulation timesteps to perform 174 16 Sample configuration files This section contains some simple example NAMD configuration files to serve as templates This file shows a simple configuration file for alanin It performs basic dynamics with no output files or special features protocol params numsteps 1000 initial config coordinates alanin pdb temperature 300K seed 12345 output params outputname tmp alanin binaryoutput no integrator params timestep 1 0 force field params structure alanin psf parameters alanin params exclude scaled1 4 1 4scaling 1 0 switching on switchdist 8 0 cutoff 12 0 pairlistdist 13 5 stepspercycle 20 175 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
254. psfgen by hand as it will probably mess up the internal numbering in the PSF file Very often the atoms you want to delete are water molecules that are either too far from the solute or else outside of the periodic box you are trying to prepare In either case VMD atom selections can be used to select the waters you want to delete For example Load a pdb and psf file into both psfgen and VMD resetpsf readpsf myfile psf coordpdb myfile pdb mol load psf myfile psf pdb myfile pdb Select waters that are more than 10 Angstroms from the protein set badwater1 atomselect top name OH2 and not within 10 of protein 29 Alternatively select waters that are outside our periodic cell set badwater2 atomselect top name OH2 and x lt 30 or x gt 30 or y lt 30 or gt 30 or z lt 30 or z gt 30 Delete the residues corresponding to the atoms we selected foreach segid badwater1 get segid resid 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
255. ptTempFreq lt steps between temperature updates gt Acceptable Values Positive integers Default Value 10 Description The number of steps between temperature updates Note that the potential energy at the current is calculated and added to the temperature energy histogram at every step e adaptTempTmin lt minimum temperature K gt Acceptable Values Positive real number Description Sets the minimum temperature to be used in the simulation e adaptTempTmax lt maximum temperature K gt Acceptable Values Positive real number Description Sets the maximum temperature to be used in the simulation e adaptTempBins lt number of temperature bins gt Acceptable Values Positive integer Default Value 1000 Description Sets the number of bins to subdivide the temperature range Each bin stores the average energy for the given temperature e adaptTempDt lt stepsize for temperature updates gt Acceptable Values Positive real numbers Default Value 107 Description Integration timestep for temperature updates This is unrelated to the simulation timestep and only scales the size of the step taken in temperature space every adaptTempFreq steps e adaptTempInFile lt adaptive tempering input filename gt Acceptable Values UNIX filename Description The input file containing restart information for adaptive tempering written out by adaptTempRestartFile 156 adaptTempRestartFile lt adaptive tempering restart filename gt
256. ptable Values UNIX filename Default Value coordinates Description PDB file to specify the LES image number of each atom If this parameter is not specified then the PDB file containing initial coordinates specified by coordinates is used e lesCol lt column of PDB file containing LES flags gt Acceptable Values X Y Z 0 or B Default Value B Description Column of the PDB file to specify the LES image number of each atom This parameter may specify any of the floating point fields of the PDB file either X Y Z occupancy or beta coupling temperature coupling A value of 0 in this column indicates that the atom is not enhanced Any other value should be a positive integer less than lesFactor 12 4 Replica exchange simulations The lib replica directory contains Tcl scripts that implement replica exchange both for parallel tempering temperature exchange and umbrella sampling exchanging collective variable biases This replaces the old Tcl server and socket connections driving a separate NAMD process for every replica used in the simulation A NAMD build based on a patched MPI build of Charm is required The included lib replica charm_replica patch has already been applied to the Charm source code included with the NAMD source code It is only needed if you obtain Charm directly from charm cs illinois edu Only temperature exchange simulations are described below To employ replicas for um brella sampling you will nee
257. ptable 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 85 9 3 Grid Forces NAMD provides the ability to specify grids describing a potential in the simulation space Each atom is affected by the potential based on its charge and its position using the potential function interpolated from the specified grid s Energy due to the grid defined field will be reported in the MISC column of the output unless a scaling factor not proportional to 1 1 1 is used NAMD allows the definition of multiple grids each with a separate set of defining parame ters This is specified using a tag field in each of the mgridforceXXX commands The tag is an alphanumeric string without spaces which identifies to which grid the specified field applies The grid file format is a subset of the DataExplorer DX file format as shown below Lines at the beginning of the file starting with a symbol are ignored as comments Variables replaced by numbers in an actual file xn yn and zn are the number of data points along each dimension xorg yorg and zorg is the origin of the grid in angstroms x 1 3 del y 1 3 del and z 1 3 del are the basis vectors which transform grid indices to coordinates in angstroms x i j k xorg
258. q0 q1 q2 q3 quadruplet if it returns a rotational quaternion Ifa colvar has periodicities or symmetries its closest image to the restraint center is considered when calculating the harmonic potential targetCenters lt harmonic Steer the restraint centers towards these targets gt Acceptable Values space separated list of colvar values Description When defined the current centers will be moved towards these values during the simulation By default the centers are moved over a total of targetNumSteps steps by a linear interpolation in the spirit of Steered MD If targetNumStages is set to a nonzero value the change is performed in discrete stages lasting targetNumSteps steps each This second mode may be used to sample successive windows in the context of an Umbrella Sampling simulation When continuing a simulation run the centers specified in the configuration file lt colvarsConfig gt will be overridden by those saved in the restart file lt colvarsInput gt To perform Steered MD in an arbitrary space of colvars it is sufficient to use this option and enable outputAppliedForce within each of the colvars involved targetForceConstant lt harmonic Change the force constant towards this value gt Acceptable Values positive decimal Description When defined the current forceConstant will be moved towards this value during the simulation Time evolution of the force constant is dictated by the targetForceExponent parameter s
259. r each restart conf file or for example just do vmd e load_all vmd This script will likely destroy anything else you are doing in VMD at the time so it is best to start with a fresh VMD clone reps vmd provides the clone _reps commmand to copy graphical representation from the top molecule to all other molecules sortreplicas found in the namd2 binary directory is a program to un shuffle replica trajec tories to place same temperature frames in the same file Usage sortreplicas lt job_output_root gt lt num_replicas gt lt runs_per_frame gt final_step where job_output_root is the job specific output base path including s or d for separate directo ries as in output s fold_alanin job1 This will be extended with d dced d history for input files and d sort ded d sort history for output files The optional final step parameter will truncate all output files after the specified step which is useful in dealing with restarts from runs that did not complete Colvars trajectory files are similarly processed if they are found A replica exchange config file should define the following Tcl variables e num replicas the number of replica simulations to use e min temp the lowest replica target temperature e max_temp the highest replica target temperature e steps_per_run the number of steps between exchange attempts e num_runs the number of runs before stopping should be divisible by runs_per_frame x frames per restar
260. r the angles of 180 degrees allowed by cosine based angles When using MARTINI the following configuration parameters should be set as indicated cosAngles on martiniSwitching on dielectric 15 0 PME off 53 e cosAngles lt enable the MARTINI cosine based angle potential function gt Acceptable Values on or off Default Value off Description Specifies whether or not the MARTINI forcefield is being used specifically cosine based angle potential function The cosine based potential will only be used for angles in CHARMM parameter files that specify the cos keyword e martiniSwitching lt enable the MARTINI Lennard Jones switching function gt Acceptable Values on or off Default Value off Description Specifies whether or not the MARTINI forcefield is being used specifically the Lennard Jones switching function e martiniDielAllow lt Allow dielectrics 15 0 for use with MARTINI gt Acceptable Values on or off Description off Allows user to specify a dielectric not equal to 15 0 ie a non standard dielectric for MARTINI 5 6 Constraints and Restraints 5 6 1 Bond constraint parameters e rigidBonds lt controls if and how ShakeH is used gt Acceptable Values none water all Default Value none Description When water is selected the hydrogen oxygen and hydrogen hydrogen dis tances in waters are constrained to the nominal length or angle given in the parameter file making the molecules completely rigid When rigidB
261. rFuncStride lt colvar Stride of the time correlation function gt Acceptable Values positive integer Default Value 1 Description Number of steps between two values of the time correlation function e corrFuncOffset lt colvar Offset of the time correlation function gt Acceptable Values positive integer Default Value 0 Description The starting time in number of steps of the time correlation function default t 0 Note the value at t 0 is always used for the normalization e corrFuncOutputFile lt colvar Output file for the time correlation function gt Acceptable Values UNIX filename Default Value lt name gt corrfunc dat Description The time correlation function is saved in this file e runAve lt colvar Calculate the running average and standard deviation gt Acceptable Values boolean Default Value off Description Whether or not the running average and standard deviation should be cal culated for this colvar e runAveLength lt colvar Length of the running average window gt Acceptable Values positive integer Default Value 1000 Description Length in number of points of the running average window e runAveStride lt colvar Stride of the running average window values gt Acceptable Values positive integer Default Value 1 Description Number of steps between two values within the running average window e runAve0utputFile lt colvar Output file for the running average and standard d
262. raction 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 monitoring the very rare case where atoms actually move more than the tolerance distance we reduce the trigger tolerance by this fraction The tolerance is increased whenever the trigger tolerance is exceeded as specified by pairlistGrow 84 9 User Defined Forces There are several ways to apply external forces to simulations with NAMD These are described below 9 1 Constant Forces NAMD provides the ability to apply constant forces to some atoms There are two parameters that control this feature e constantForce lt Apply constant forces gt Acceptable Values yes or no Default Value no Description Specifies whether or not constant forces are applied e con
263. rals are generated automatically unless auto none is added which is required to build residues of water The commands first and last may be used to change the default patches for the ends of the chain The structure is built when the closing is encountered and some errors regarding the first and last residue are normal 5 Patch protein segment Some patch residues those not used to begin or end a chain are applied after the segment is built These contain all angle and dihedral terms explicitly since they were already generated In this case we apply the patch for a disulfide link three separate times 6 Read protein coordinates from PDB file The same file used to generate the sequence is now read to extract coordinates In the residue ILE the atom CD is called CD1 in the pdb file so we use pdbalias atom to define the correct name If the segment names in the pdb file match the name we gave in the segment statement then we don t need to specify it again in this case we do specify the segment so that all atoms in the pdb file must belong to the segment 7 Build water segment Build a segment for the crystal waters The residue type for 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
264. ranges from approximately 0 all inter atomic distances much larger than the cutoff to Ngroup1 Ngroup1 1 2 all distances within the cutoff For performance reasons group1 should be of limited size because the cost of the loop over all pairs grows as N roupi Component hBond hydrogen bond between two atoms The hBond block defines a hydrogen bond implemented as a coordination number eq 37 between the donor and the acceptor atoms Therefore it accepts the same options cutoff with a different default value of 3 3 A expNumer with a default value of 6 and expDenom with a default value of 8 Unlike coordNun it requires two atom numbers acceptor and donor to be defined It returns an adimensional number with values between 0 acceptor and donor far outside the cutoff distance and 1 acceptor and donor much closer than the cutoff Component rmsd root mean square displacement RMSD with respect to a reference structure The block rmsd defines the root mean square replacement RMSD of a group of atoms with respect to a reference structure For each set of coordinates x t xX2 t x t ref H the colvar component rmsd calculates the optimal rotation U gt that best superimposes the coordinates x t onto a set of reference coordinates py Both the current and the a f reference coordinates are centered on their centers of geometry Xcog t and xe The root mean square displacement is the
265. rature data on the cold and warm degrees of freedom Four additional quantities are listed on the ETITLE and ENERGY lines DRUDECOM gives the temperature for the warm center of mass degrees of freedom DRUDEBOND gives the temperature for the cold Drude oscillator degrees of freedom DRCOMAVG gives the average temperature averaged since the previously reported temperature for the warm center of mass degrees of freedom DRBONDAVG gives the average temperature averaged since the previously reported temperature for the cold Drude oscillator degrees of freedom The energies resulting from the Drude oscillators and the anisotropic interactions are summed into the BOND energy The energies resulting from the LPs and the screened Coulomb interactions of Thole are summed into the ELECT energy 5 4 3 Drude force field parameters The Drude model should be used with the Langevin thermostat enabled Langevin on Doing so permits the use of normal sized time steps e g 1 fs The Drude model is also compatible with constant pressure simulation using the Langevin piston Long range electrostatics may be calculated using PME The nonbonded exclusions should generally be set to use either the 1 3 exclusion policy exclude 1 3 or the scaled 1 4 exclusion policy exclude scaled1 4 The Drude water model SWM4 NDP is a 5 site model with four charge sites and a nega tively charged Drude particle 40 with the particles ordered in the input files as oxyg
266. rces 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 104 Description Atom forces are read from this file after extForcesCommand in run The format is one line of atomid replace fx fy fz for every atom followed by the energy on a line by itself and then optionally three lines of the virial v xx v xy v xz v yx v yy v yz v zx v zy v zz where e g v xy fx y for a non periodic force The atomid starts at 1 not 0 and all atoms must be present and in order The energy is added to the MISC output field The replace flag should be 1 if the external program force should replace the forces calculated by NAMD for that atom and 0 if the forces should be added For best performance the file should be in tmp and not on a network mounted filesystem 105 10 Collective Variable based Calculations In today s molecular dynamics simulations it is of
267. rd ramd The default values for these parameters are only given as guidance They are likely not to be suitable for other systems than those the scripts were tested on e ramd debugLevel lt Set debug level of RAMD gt Acceptable Values integer value Default Value 0 Description Activates verbose output if set to an integer greater than 0 Should be used only for testing purposes because the very dense output is full of information only relevant for debugging ramd mdStart lt Start RAMD MD with MD or RAMD gt Acceptable Values yes or no Default Value no Description Specifies if combined RAMD MD simulation starts with MD or RAMD steps ignored if pure RAMD simulation is performed Should be set to yes if initial MD steps are desired e ramd ramdSteps lt Set number steps in RAMD block gt Acceptable Values positive integer Default Value 50 Description Specifies the number of steps in 1 RAMD block the simulations are evaluated every ramdSteps steps e ramd mdSteps lt Set number steps in MD block gt Acceptable Values positive integer Default Value 0 162 Description Specifies the number of steps in 1 standard MD block in combined RAMD MD simulations the RAMD blocks are evaluated every ramdSteps the MD blocks every mdSteps steps Default of O gives pure RAMD simulation ramd accel lt Set acceleration energy gt Acceptable Values positive decimal Default Value 0 25 Descript
268. rdinates guesscoord 10 Write structure and coordinate files writepsf output bpti psf writepdb output bpti pdb End of psfgen commands ENDMOL Step by step explanation of the script 1 Split input PDB file into segments 6PTI pdb is the original file from the Protein Data Bank It contains a single chain of protein and some PO4 and H20 HETATM records Since each segment must have a separate input file we remove all non protein atom records using grep If there were multiple chains we would have to split the file by hand Create a second file containing only waters 2 Embed the psfgen commands in this script Run the psfgen program taking everything until ENDMOL as input You may run psfgen interactively as well Since psfgen is built on a Tcl interpreter you may use loops variables etc but you must use for variables when inside a shell script If you want run psfgen and enter the following commands manually 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 dihed
269. re usually neglected except by rmsd and eigenvector e refPositions lt atom group Reference positions A gt Acceptable Values space separated list of x y z triplets Description If either centerReference or rotateReference is on these coordinates are used to determine the center of mass translation and the optimal rotation respectively In the latter case the list must also be of the same length as this atom group e refPositionsFile lt atom group File with reference positions gt Acceptable Values UNIX filename Description If either centerReference or rotateReference is on the coordinates from this file are used to determine the center of geometry translation and the optimal rotation between them and the current coordinates of the group This file can either contain as many atoms as the group in which case all of the ATOM records are read or ii a larger number of atoms In the second case coordinates will be selected either according to flags in column refPositionsCol or if that parameter is not specified by index using the list of atom indices belonging to the atom group In a typical application a PDB file containing both atom flags and reference coordinates is prepared and provided as both atomsFile and refPositionsFile while the flag column is passed to atomsCol and refPositionsCol 127 e refPositionsCol lt atom group Column to use in the PDB file gt Acceptable Values X Y Z 0 or B Descriptio
270. reen an atom Though alphaCutoff can bet set to be larger or shorter than cutoff since atom forces are more sensitive to changes in position than changes in Born radius user s should generally set alphaCutoff to be shorter than cutoff e SASA lt whether or not to calculate SASA gt Acceptable Values on or off Default Value off Description The nonpolar hydrophobic energy contribution from implicit solvent is calculated it is proportional to the solvent accessible surface area which is calculated by the Linear Combination of Pairwise Overlap LCPO method 69 e surfaceTension lt surface tension of hydrophobic gt Acceptable Values positive decimal Default Value 0 005 kcal mol A Description Surface tension used when calculating SASA Enonpolar surfaceTension x surfaceArea Below is a sample excerpt from a NAMD config file for nonbonded and multistep parameters when using GBIS and SASA GBIS parameters GBIS on ionConcentration 0 3 alphaCutoff 14 nonbonded parameters switching on switchdist 15 cutoff 16 pairlistdist 18 hydrophobic energy sasa on surfaceTension 0 006 multistep parameters timestep 1 nonbondedFreq 2 fullElectFrequency 4 64 7 Standard Minimization and Dynamics Parameters 7 1 Boundary Conditions In addition to periodic boundary conditions NAMD provides spherical and cylindrical boundary potentials to contain atoms in a given volume To apply more general boundary potentials written in T
271. regimes are O Tij gt Pret Pjs sphere j beyond cutoff I rij te Pjs sphere j partially within cutoff Il rij gt 4pjs artificial regime for smoothing Regimes 4 III rij gt piot pjs spheres not overlapping 17 IV rij gt pio pjs spheres overlapping V pio lt Pjs sphere i inside sphere j VI otherwise sphere j inside sphere j 60 and the values of H are 0 0 1 2155 1 2 Tu Bis fis I Sra E Pi a ee Fis 2 1n 2 Pos Pj po pe TL te apis bse d e Tij Tij 2 re E r2 TN 1 Pjs Tij Pjs Hij HI 2 r s 7 rig tPjs 1 1 1 2 2 _ 2 1 1 Pio IV j Pio 2 Eo n Pio p rij tPjs Tij In Tij Pjs V 1 Pjs ln Pis Tij 2 ij Ps aa ay E Tij Pjs VI 0 18 Below are defined the derivatives of the above functions which are required for force calculations OEij _ k ao enpatia Orij fij Orij fh Orig OD oR gt Of Orij s expide Orij O fij zi Tij 1 r Ori o fij i 1E E d a d TEE E 1 tanh 8 BYR VWF 8 2910 3008 T ij d k dH y drij w po 2 drij KEN OH dry 7 Pro 2 Orn drij OH OA A OK bu OF bi k d api 7 Sk P 1 tanh Sui Bu y8 6 284 360 La dri Pi zi a j ig 32 1 tanh 5 py 703 5 281 3047 Se BH OF 1 keqiqj Dij a a e am aa ca LRE exp k fij Diz Qa i ex ri da T Qj 2 j Es E bs fij i 4 a 400 61 19 20 21 22 23
272. rids when reading a state file gt Acceptable Values boolean Default Value off Description When restarting from a state file the grid s parameters boundaries and widths saved in the state file override those in the configuration file Enabling this option forces the grids to match those in the current configuration file The following options define metadynamics calculations with more than one replica e multipleReplicas lt metadynamics Multiple replicas metadynamics gt Acceptable Values boolean 137 Default Value off Description If this option is on multiple independent replica of the same sys tem can be run at the same time and their hills will be combined to obtain a single PMF 52 Replicas are identified by the value of replicaID Communica tion is done by files each replica of NAMD must be able to read the files cre ated by the others whose paths are communicated through the file replicasRegistry This file and the files listed in it are read every replicaUpdateFrequency steps Every time the colvars state file is written colvarsRestartFrequency the file lt outputName gt colvars lt name gt lt replicaID gt state is also written con taining the state of the metadynamics bias for replicaID In the time steps between colvarsRestartFrequency new hills are temporarily written to the file lt outputName gt colvars lt name gt lt replicaID gt hills which serves as communication buffer Thes
273. riodic 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 25 rigidBonds all tol 0 0005 rigidTolerance 0 0005 Default is 0 00001 nstlim 500 numsteps 500 Num of total steps ntpr 50 outputEnergies 50 Energy output frequency ntwr 100 restartfreq 100 Restart file frequency ntwx 100 DCDfreq 100 Trajectory file frequency dt 0 001 timestep 1 in unit of fs This is default tempi 300 temperature 300 Initial temp for velocity assignment cut 9 cutoff 9 switching off Turn off the switching functions gend gewald PME on Use PME for electrostatic calculation Orthogonal periodic box size a 62 23 cellBasisVector1i 62 23 0 O b 62 23 cellBasisVector2 O 62 23 0 c 62 23 cellBasisVector3 O O 62 23 nfft1 64 PMEGridSizeX 64 nfft2 64 PMEGridSizeY 64 nfft3 64 PMEGridSizeZ 64 ischrgd 1 NAMD doesn t force neutralization of charge gend amber on Specify this is AMBER force field parmfile FILENAME Input PARM file ambercoor FILENAME Input coordinate file outputname PREFIX Prefix of output files exclude scaled1 4 1 4scaling 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 NA
274. rmm 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 coordpdb May call multiple times coord lt segid gt lt resid gt lt atomname gt lt z y z gt Purpose Set coordinates for a single atom Arguments lt segid gt Segment ID of target atom lt resid gt Residue ID of target atom
275. roups will be transformed by the matrices in their own symmetryMatrixFile and averaged separetely from other groups The designation in the occupancy column should be an integer value starting at 1 and proceeding in ascending order mirroring the order of the corresponding matrix file within the configuration file e g the first symmetryMatrixFile contains the matrices for symmetry group 1 The value in the atom s beta column represents its monomer designa tion This should be an integer value starting at 1 and proceeding in ascending order relative to the order of the corresponding transformation matrix found in the symmetry group s symmetryMatrixFile If an atom is contained in more than one symmetry group additional pdb files can be listed These pdb files should follow the same rules as the first one unique group and monomer identifiers in increasing order e symmetryMatrixFile lt File for transformation matrices gt Acceptable Values Path to matrix file Description The symmetryMatrixFile is a path to a file that contains a list of trans formation matrices to make the monomers overlap The file should contain one and only one matrix for each monomer in the order of monomer ID designated in the symmetryFile Each symmetry group should have its own symmetryMatrixFile file containing only the ma trices used by the monomers in that group These should be formatted with spaces between columns and NO spaces between rows as follows 1
276. rovided within the metadynamics block The only mandatory parameter is the colvars option listing all the variables to which this bias is applied Note multidimensional PMFs are obtained with one metadynamics instance applied to all the colvars and not with multiple instances applied to individual colvars The following two options have default values that are reasonable in typical situations but it is strongly recommended that the user chooses them according to the above discussion on the diffusion times of the variables TE e hillWeight lt metadynamics Height of each hill kcal mol gt Acceptable Values positive decimal Default Value 0 01 Description This option sets the height W of the hills that are added during this run Lower values provide more accurate sampling at the price of longer simulation times to com plete a PMF calculation 136 e newHillFrequency lt metadynamics Frequency of hill creation gt Acceptable Values positive integer Default Value 100 Description This option sets the number of integration steps after which a new hill is added to the metadynamics potential Its value determines the parameter t in eq 52 Higher values provide more accurate sampling at the price of longer simulation times to complete a PMF calculation The following options control the performance of metadynamics calculations but do not affect the results e useGrids lt metadynamics Interpolate the hills with grids
277. s set num_replicas 8 set min_temp 300 set max_temp 600 set steps_per_run 1000 set num_runs 10000 num_runs should be divisible by runs_per_frame frames_per_restart set runs_per_frame 10 set frames_per_restart 10 set namd_config_file alanin_base namd set output_root output s fold_alanin directories must exist the following used only by show_replicas vmd set psf_file alanin psf set initial_pdb_file unfolded pdb set fit_pdb_file alanin pdb 12 5 Random acceleration molecular dynamics simulations The lib ramd directory stores the tcl scripts and the example files for the implementation of the Random Acceleration Molecular Dynamics RAMD simulation method in NAMD The RAMD method can be used to carry out molecular dynamics MD simulations with an additional randomly oriented acceleration applied to the center of mass of one group of atoms referred below as ligand in the system It can for example be used to identify egress routes for a ligand from a buried protein binding site Since its original implementation in the ARGOS ref 1 2 program the method has 161 been also implemented in AMBER 8 ref 3 and CHARMM ref 4 The first implementation of RAMD in NAMD using a tcl script available as supplementary material in ref 6 provided only limited functionality compared to the AMBER 8 implementation In the current implementation the RAMD method can be performed in 2 flavors i pure
278. s Linux Mac OS X or other Unix with only ethernet net working hopefully gigabit NAMD uses the Charm native communications layer and the pro gram charmrun to launch namd2 processes for parallel runs either exclusively on the local machine with the local option or on other hosts as specified by a nodelist file The namd2 binaries for these platforms can also be run directly known as standalone mode for single process runs 17 1 Individual Windows Linux Mac OS X or Other Unix Workstations Individual workstations use the same version of NAMD as workstation networks but running NAMD is much easier If your machine has only one processor core you can run the any non MPI namd2 binary directly namd2 lt configfile gt Windows Mac OX X Intel and Linux x86_64 multicore released binaries are based on mul ticore builds of Charm that can run multiple threads These multicore builds lack a network layer so they can only be used on a single machine For best performance use one thread per processor with the p option namd2 p lt procs gt lt configfile gt For other multiprocessor workstations the included charmrun program is needed to run multiple namd2 processes The local option is also required to specify that only the local machine is being used charmrun namd2 local p lt procs gt lt configfile gt You may need to specify the full path to the namd2 binary 17 2 Windows Clusters and Workstation Networks
279. s SMD and Umbrella Sampling US via a flexible harmonic restraint bias see 10 3 3 e calculate statistical properties of the colvars such as their running averages and standard deviations time correlation functions and multidimensional histograms without the need to save very large trajectory files e compute collective variable values from existing coordinates e g an MD trajectory use NAMD s coorfile read command and perform a 0 timestep run for each set of coordinates as illustrated in 16 10 1 General parameters and input output files The structure of a typical colvars configuration is represented in Figure 6 Each colvar is a com bination of one or more components see 10 2 which are functions of several atomic coordinates Many different biasing or analysis methods can be applied to the same colvars But care should be taken that certain methods such as free energy reconstruction do not produce correct results when other biases are adding forces to their colvars 10 1 1 NAMD parameters To enable a colvar calculation two parameters should be added to the NAMD configuration file must set three when restarting a previous run The features described in this section were contributed by Giacomo Fiorin ICMS Temple University Philadel phia PA USA and J r me H nin LISM CNRS Marseille France Please send feedback and suggestions to the NAMD mailing list 106 biases colvars components distance d
280. s 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 97 e IMDignore lt ignore interactive steering forces gt Acceptable Values yes or no Default Value no Description If yes NAMD will ignore any steering forces generated by VMD to allow a simulation to be monitored without the possibility of perturbing it 9 10 Tcl Forces and Analysis NAMD provides a limited Tcl scripting interface designed for applying forces and performing on the fly analysis This interface is efficient if only a few coordinates either of individual atoms or centers of mass of groups of atoms are needed In addition information must be requested one timestep in advance To app
281. s allow performance tuning parameters to be set based on the parallel execution environment e The reinitvels command reinitializes velocities to a random distribution based on the given temperature e The rescalevels command rescales velocities by the given factor e The reloadCharges command reads new atomic charges from the given file which should contain one number for each atom separated by spaces and or line breaks e The consForceConfig command takes a list of 0 based atom indices and a list of forces which replace the existing set of constant forces constantForce must be on e The measure command allows user programmed calculations to be executed in order to facilitate automated methods For example to revert or change a parameter A number of measure commands are included in the NAMD binary the module has been designed to make it easy for users to add additional measure commands e The coorfile command allows NAMD to perform force and energy analysis on trajectory files coorfile open dcd filename opens the specified DCD file for reading coorfile read reads the next frame in the opened DCD file replacing 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 c
282. s directly This implements the extended Lagrangian formalism used in some metadynamics simula tions 33 The energy associated with the extended degree of freedom is reported under the MISC title in NAMD s energy output e extendedFluctuation lt colvar Standard deviation between the colvar and the fictitious particle colvar unit gt Acceptable Values positive decimal Default Value 0 2 x width Description Defines the spring stiffness for the extendedLagrangian mode by setting the typical deviation between the colvar and the extended degree of freedom due to thermal fluctuation The spring force constant is calculated internally as kgT 0 where is the value of extendedFluctuation 113 extendedTimeConstant lt colvar Oscillation period of the fictitious particle fs gt Acceptable Values positive decimal Default Value 40 0 x timestep Description Defines the inertial mass of the fictitious particle by setting the oscillation period of the harmonic oscillator formed by the fictitious particle and the spring The period should be much larger than the MD time step to ensure accurate integration of the extended particle s equation of motion The fictitious mass is calculated internally as kgT 7 270 where 7 is the period and is the typical fluctuation see above extendedTemp lt colvar Temperature for the extended degree of freedom K gt Acceptable Values positive decimal Default Value NAMD thermostat te
283. s 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 9b3 binaries are available for download for the following platforms e Windows XP etc on x86 or x86 64 processors e Mac OS X on Intel processors e Linux on x86 or x86 64 processors e Linux on x86 64 processors with NVIDIA GPUs CUDA NAMD may be compiled for the following additional platforms e Cray XT XE XK e IBM Blue Gene L P Q e Linux or AIX on POWER processors e Solaris on x86 64 processors 18 3 Installing NAMD A NAMD binary distribution need only be untarred or unzipped and can be run directly in the resulting directory When building from source code make release will generate a self contained directory and tar gz or zip archive that can be moved to the desired installation location Windows and CUDA builds include Tcl dll and CUDA so files that must be in the dynamic library path 18 4 Compiling NAMD We provide complete and optimized binaries for all common platforms to which NAMD has been ported It should not be necessary for you to compile NAMD unless you wish to add or mod ify features or to improve performance by 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
284. s see Section 5 2 If switching is set to on then switchdist must also be defined e vdwForceSwitching lt use force switching for VDW gt Acceptable Values on or off Default Value off Description If both switching and vdwForceSwitching are set to on then CHARMM force switching is used for van der Waals forces LJcorrection as implemented is incon sistent with vdwForceSwitching e switchdist lt distance at which to activate switching splitting function for electrostatic 45 and van der Waals calculations A gt Acceptable Values positive decimal lt cutoff Description Distance at which the switching function should begin to take effect This parameter only has meaning if switching is set to on The value of switchdist must be less than or equal to the value of cutoff since the switching function is only applied on the range from switchdist to cutoff For a complete description of the non bonded force parameters see Section 5 2 exclude lt non bonded exclusion policy to use gt Acceptable Values none 1 2 1 3 1 4 or scaled1 4 Description This parameter specifies which pairs of bonded atoms should be excluded from non bonded interactions With the value of none no bonded pairs of atoms will be excluded With the value of 1 2 all atom pairs that are directly connected via a linear bond will be excluded With the value of 1 3 all 1 2 pairs will be excluded along with all pairs of atoms that are bonded to a common
285. s the parameters for calculating the radius of gyration of a group of atomic positions x1 t x2 t xy t with respect to their center of geometry Xcog t dl 3 Reyr N 5 x t zu Xcog t 41 i 1 This component must contain one atoms block to define the atom group and returns a positive number expressed in Component orientation orientation from reference coordinates The block orientation returns the same optimal rotation used in the rmsd component to superimpose the coordinates x t onto a set of reference coordinates py Such component returns a four dimensional vector q qo q1 92 93 with gt gt q 1 this quaternion expresses the optimal rota tion x t gt xD according to the formalism in reference 16 The quaternion qo q1 42 93 can also be written as cos 9 2 sin 2 u where 0 is the angle and u the normalized axis of rotation for example a rotation of 90 around the z axis should be expressed as 0 707 0 0 0 0 0 707 The script quaternion2rmatrix tcl provides Tcl functions for converting to and from a 4 x 4 rotation matrix in a format suitable for usage in VMD The component accepts all the options of rmsd atoms refPositions refPositionsFile and refPositionsCol in addition to e closestToQuaternion lt orientation Reference rotation gt Acceptable Values q0 qi q2 q3 quadruplet Default Value 1 0 0 0 0 0 0 0 null rotation Descripti
286. sForceFile 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 consforcefile is optional constant forces may be specified or updated between runs by using the consForceConfig command e consForceScaling lt Scaling factor for constant forces gt Acceptable Values decimal Default Value 1 0 Description Scaling factor by which constant forces are multiplied May be changed between run commands 9 2 External Electric Field NAMD provides the ability to apply a constant electric field to the molecular system being simu lated Energy due to the external field will be reported in the MISC column and 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 Acce
287. se before pairlists will be enabled on fewer processors small local pairlists are generated and recycled rather than being saved the default is pairlistMinProcs 1 This is a per simulation rather than a compile time option because memory usage is molecule dependent Additional information on reducing memory usage may be found at http www ks uiuc edu Research namd wiki index cgi NamdMemoryReduction 17 12 Improving Parallel Scaling While NAMD is designed to be a scalable program particularly for simulations of 100 000 atoms or more at some point adding additional processors to a simulation will provide little or no extra performance If you are lucky enough to have access to a parallel machine you should measure NAMD s parallel speedup for a variety of processor counts when running your particular simulation The easiest and most accurate way to do this is to look at the Benchmark time lines that are printed after 20 and 25 cycles usually less than 500 steps You can monitor performance during the entire simulation by adding output Timing steps to your configuration file but be careful to look at the wall time rather than CPU time fields on the TIMING output lines produced For an external measure of performance you should run simulations of both 25 and 50 cycles see the stepspercycle parameter and base your estimate on the additional time needed for the longer simulation in order to exclude startup co
288. sed in the calculation of boost energy for the Total Dihedral potential This option is only available when accelMDdual is turned on accelMDFirstStep lt First accelerated MD step gt Acceptable Values Zero or positive integer Default Value 0 Description Accelerated MD will only be performed when the current step is equal to or higher than accelMDFirstStep and equal to or lower than accelMDLastStep Otherwise regular MD will be performed accelMDLastStep lt Last accelerated MD step gt Acceptable Values Zero or positive integer Default Value 0 Description Accelerated MD will only be performed when the current step is equal to or higher than accelMDFirstStep and equal to or lower than accelMDLastStep Otherwise regular MD will be performed Note that the accelMDLastStep parameter only has an effect when it is positive When accelMDLastStep is set to zero the default aMD is open ended and will be performed till the end of the simulation accelMDOutFreq lt Frequency in steps of aMD output gt Acceptable Values Positive integer Default Value 1 Description An aMD output line will be printed to the log file at the frequency specified by accelMDOutFreq The aMD output will contain the boost potential dV at the current timestep the average boost potential 1W AVG since the last aMD output and various potential energy values at the current timestep The boost potential dV can be used to reconstruct the ensemb
289. select the atoms involved Here is an example configuration for an atom group called myatoms which makes use of the most common keywords atom group definition myatoms add atoms 1 2 and 3 to this group note numbers start from 1 atomNumbers 125 123 add all the atoms with occupancy 2 in the file atoms pdb atomsFile atoms pdb atomsCol 0 atomsColValue 2 0 add all the C alphas within residues 11 to 20 of segments PR1 and PR2 psfSegID PR1 PR2 atomNameResidueRange CA 11 20 atomNameResidueRange CA 11 20 For any atom group the available options are atomNumbers lt atom group List of atom numbers gt Acceptable Values space separated list of positive integers Description This option adds to the group all the atoms whose numbers are in the list Atom numbering starts from 1 atomNumbersRange lt atom group Atoms within a number range gt Acceptable Values lt Starting number gt lt Ending number gt Description This option adds to the group all the atoms whose numbers are within the range specified It can be used multiple times for the same group Atom numbering starts from 1 May be repeated atomNameResidueRange lt atom group Named atoms within a range of residue numbers gt Acceptable Values lt Atom name gt lt Starting residue gt lt Ending residue gt Description This option adds to the group all the atoms with the provided name within residues in the given range May b
290. springs for rotating constraints leads to the system lagging behind the reference positions and then the force is applied along a direction different from the ideal direction along the circular path Pulling on N atoms at the same time with a spring of stiffness K amounts to pulling on the whole system by a spring of stiffness NK so the overall behavior of the system is as if you are pulling with a very stiff spring if N is large In both moving and rotating constraints the force constant that you specify in the constraints pdb file is multiplied by 2 for the force calculation i e if you specified K 0 5 keal mol A in the pdb file the force actually calculated is F 2kK R X 1 keal mol A R X SMD feature of namd2 does the calculation without multiplication of the force constant specified in the config file by 2 e rotConstraints lt Are rotating constraints active gt Acceptable Values on or off Default Value off Description Should rotating restraints be applied to the system If set to on then rotConsAxis rotConsPivot and rotConsVel must be defined May not be used with movingConstraints e rotConsAxis lt Axis of rotation gt Acceptable Values vector may be unnormalized Description Axis of rotation Can be any vector It gets normalized before use If the vector is 0 no rotation will be performed but the calculations will still be done e rotConsPivot lt Pivot point of rotation gt Acceptable Values pos
291. ssure simulation using a modified Nos Hoover method in which Langevin dynamics is used to control fluctuations in the barostat This method should be combined with a method of temperature control such as Langevin dynamics in order to simulate the NPT 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 78 Constant pressure molecular dynamics simulation The Langevin piston method J Chem Phys 103 11 1995 The equations of motion are r p m er p F ep gp R V 3Ve e 3V W P Po gee Re W W 3N7r kT 2mgkT h oscillationperiod ER 2WgekT h A a N V II 4 Here W is the mass of piston R is noise on atoms and Re is the noise on the piston The user specifies the desired pressure oscillation and decay times of the piston and tempera ture of the piston The compressibility of the system is not required In addition the user specifies the damping coefficients and temperature of the atoms for Langevin dynamics The following parameters are used to define the algorithm e LangevinPiston lt use Langevin piston pressure control gt Acceptable Values on or off Default V
292. st rapidly convergent it is sufficient for most applications There are only two parameters for minimization one to activate minimization and another to specify the maximum movement of any atom e velocityQuenching lt Perform old style energy minimization gt Acceptable Values on or off Default Value off Description Turns slow energy minimization on or off e maximumMove lt maximum distance an atom can move during each step A gt Acceptable Values positive decimal Default Value 0 75 x cutoff stepsPerCycle Description Maximum distance that an atom can move during any single timestep of minimization This is to insure that atoms do not go flying off into space during the first few timesteps when the largest energy conflicts are resolved 7 3 Dynamics 7 3 1 Timestep parameters e numsteps lt number of timesteps gt Acceptable Values positive integer 69 Description The number of simulation timesteps to be performed An integer greater than 0 is acceptable The total amount of simulation time is numsteps x timestep e timestep lt timestep size fs gt Acceptable Values non negative decimal Default Value 1 0 Description The timestep size to use when integrating each step of the simulation The value is specified in femtoseconds e firsttimestep lt starting timestep value gt Acceptable Values non negative integer Default Value 0 Description The number of the first timestep This value is typically used o
293. start Description The prefix to use for restart filenames NAMD produces restart files that store the current positions and velocities of all atoms at some step of the simulation This option specifies the prefix to use for restart files in the same way that outputname specifies a filename prefix for the final positions and velocities If restartname is defined then the parameter restartfreq must also be defined restartfreq lt frequency of restart file generation gt Acceptable Values positive integer Description The number of timesteps between the generation of restart files restartsave lt use timestep in restart filenames gt Acceptable Values yes or no Default Value no Description Appends the current timestep to the restart filename prefix producing a sequence of restart files rather than only the last version written binaryrestart lt use binary restart files gt Acceptable Values yes or no Default Value yes Description Enables the use of binary restart files If this option is not set to no then the restart files will be written in binary rather than PDB format Binary files preserve more accuracy between NAMD restarts than ASCII PDB files but the binary files are not guaranteed to be transportable between computer architectures The atom count record is used to detect wrong endian files which works for most atom counts The utility program flipbinpdb is provided to reformat these files if necessary DCDfi
294. stepspercycle and pairlistspercycle may help but it is important to benchmark The pairlist distance will adjust automatically and one pairlist per ten steps is a good ratio NAMD should scale very well when the number of patches multiply the dimensions of the patch grid is larger or rougly the same as the number of processors If this is not the case it may be possible to improve scaling by adding twoAwayX yes to the config file which roughly doubles the number of patches Similar options twoAwayY and twoAwayZ also exist and may be used in combination but this greatly increases the number of compute objects twoAwayX has the unique advantage of also improving the scalability of PME Additional performance tuning suggestions and options are described at http www ks uiuc edu Research namd wiki NamdPerformanceTuning 187 18 NAMD Availability and Installation NAMD is distributed freely for non profit use NAMD 2 9b3 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 9b3 18 1 How to obtain NAMD NAMD may be downloaded from http www ks uiuc edu Research namd You will be re quired to provide minimal registration information and agree to a license before receiving access to the software Both source and binary distributions are available 18 2 Platform
295. sts and allow for initial load balancing Multicore builds scale well within a single node On machines with more than 32 cores it may be necessary to add a communication thread and run on one fewer core than the machine has On a 48 core machine this would be run as namd2 p47 commthread Performance may also benefit from setting CPU affinity using the setcpuaffinity pemap jmapj commap jmapj options described in CPU Affinity above Experimentation is needed We provide standard UDP TCP and ibverbs InfiniBand precompiled binaries for Linux clusters The TCP version may be faster on some networks but the UDP version now performs 186 well on gigabit ethernet The ibverbs version should be used on any cluster with InfiniBand and for any other high speed network you should compile an MPI version SMP builds generally do not scale as well across nodes as single threaded non SMP builds because the communication thread is both a bottleneck and occupies a core that could otherwise be used for computation As such they should only be used to reduce memory consumption or if for scaling reasons you are not using all of the cores on a node anyway and you should run benchmarks to determine the optimal configuration Extremely short cycle lengths less than 10 steps will limit parallel scaling since the atom migration at the end of each cycle sends many more messages than a normal force evaluation Increasing margin from 0 to 1 while doubling
296. switch from RAMD to MD is applied if dr gt rRamdMin A switch from MD to RAMD is applied if i dm lt rMdMin and d gt 0 acceleration direction is kept from previous RAMD block ii if dm lt rMdMin and d lt 0 acceleration direction is changed iii if dm gt rMdMin and d lt 0 acceleration direction is changed In all other case a switch is not applied 164 13 Hybrid MD Go Simulation 13 1 Hybrid MD Go model NAMD incorporates a hybrid MD Go model hereby referred to as Go to study the conformation changes in biomolecular systems The method replaces the physical based nonbonded interactions with a smoother knowledge based potential energy surface Bonded interactions are taken from the classical force fields By removing energetic traps along a MD trajectory the system will be able to sample states not normally accessible to classical MD simulations 13 2 Hybrid MD Go considerations Typically Go simulations are conducted in the absence of solvent and with electrostatic and van der Waals forces in the system turned off to improve conformational space exploration Due to the current implementation of Go the partial charges and van der Waals radii need to be set to zero in the psf and parameter file to remove the physical nonbonded interactions Additionally NAMD uses a reference PDB structure to construct the Go pairwise potential between atoms Finally the
297. t e runs per_frame the number of runs between trajectory outputs e frames _per_restart the number of frames between restart outputs e namd config file the NAMD config file containing all parameters needed for the sim ulation except seed langevin langevinTemp outputEnergies outputname dcdFreq temperature bincoordinates binvelocities or extendedSystem which are provided by replica namd e output_root the directory fileroot for output files optionally including a s that is re placed with the replica index to use multiple output directories e psf file the psf file for show_replicas vmd 160 e initial_pdb_file the initial coordinate pdb file for show_replicas vmd e fit_pdb_file the coodinates that frames are fit to by show_replicas vmd e g a folded structure The lib replica example directory contains all files needed to fold a 66 atom model of a deca alanine helix e alanin base namd basic config options for NAMD e alanin params parameters e alanin psf structure e unfolded pdb initial coordinates e alanin pdb folded structure for fitting in show_replicas vmd e fold_alanin conf config file for replica_exchange tcl script e job0 conf config file to start alanin folding for 10 ns e job1 conf config file to continue alanin folding another 10 ns and e load_all vmd load all output into VMD and color by replica index The fold_alanin conf config file contains the following setting
298. t tc1BC on tclBCScript proc veclen2 vi H foreach x1 y1 z1 v1 break return expr x1 x1 y1x y1 z1 z1 wrapmode input wrapmode cell wrapmode nearest wrapmode patch the default 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 103 set tol 2 0 set cut2 expr R tol R tol while nextatom addenergy 1 monitor how many atoms are checked set rvec getcoord set r2 veclen2 rvec if r2 lt cut2 dropatom continue if r2 gt R2 addenergy 1 monitor how many atoms are affected set r expr sqrt r2 addenergy expr K r R r R addforce vecscale rvec expr 2 K r R r tclBCArgs 48 0 10 0 9 12 External Program Forces This feature allows an external program to be called to calculate forces at every force evaluation taking all atom coordinates as input e extForces lt Apply external program forces gt 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 fo
299. t Acceptable Values positive integer Description The number of timesteps between the writing of velocities to the trajectory file The initial velocities will not be included in the trajectory file Velocities in DCD files are stored in NAMD internal units and must be multiplied by PDBVELFACTOR 20 45482706 to convert to A ps forceDCDfile lt force trajectory output file gt Acceptable Values UNIX filename Default Value outputname forcedcd Description The binary DCD force trajectory filename This file stores the trajectory of all atom forces using the same format binary DCD as X PLOR If forceDCDfile is defined then forceDCDfreq must also be defined forceDCDfreq lt timesteps between writing force to trajectory file gt Acceptable Values positive integer Description The number of timesteps between the writing of forces to the trajectory file The initial forces will not be included in the trajectory file Forces in DCD files are stored in kcal mol A In the current implementation only those forces that are evaluated during the timestep that a frame is written are included in that frame This is different from the behavior of TclForces and is likely to change based on user feedback For this reason it is strongly recommended that forceDCDfreq be a multiple of fullElectFrequency 3 2 3 Standard output NAMD logs a variety of summary information to standard output The standard units used by NAMD are Angstroms for length kcal
300. t for commercial use see Paragraph 7 below without a fee Licensee agrees to reproduce the copyright notice and other proprietary markings on all copies of the Soft ware Licensee has no right to transfer or sublicense the Software to any unauthorized person or entity However Licensee does have the right to make complimentary works that interoperate with NAMD to freely distribute such complimentary works and to direct others to the 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
301. te data for most other molecular dynamics programs as well including X PLOR and CHARMM A full description of this file format can be obtained from the PDB web site at http www rcsb org pdb Positions in PDB files are stored in A Velocities in PDB files are stored in A ps and may be divided by PDBVELFAC TOR 20 45482706 to convert to the NAMD internal units used in DCD and NAMD binary files Forces in PDB files are stored in kcal mol A NAMD binary files below should be preferred to PDB files in most cases due to their higher precision 3 1 2 X PLOR format PSF files NAMD uses the same protein structure files that X PLOR does These files may be generated with psfgen VMD X PLOR or CHARMM CHARMM can generate an X PLOR format PSF file with the command write psf card xplor 3 1 3 CHARMM19 CHARMM22 and CHARMM27 parameter files NAMD supports CHARMM19 CHARMM22 and CHARMM27 parameter files in both X PLOR and CHARMM formats X PLOR format is the default CHARMM format parameter files may be used given the parameter paraTypeCharmm on For a full description of the format of commands used in these files see the X PLOR and CHARMM User s Manual 10 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 The file readers in NAMD and VMD can detect and adapt to the endi
302. te 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 102 getcell Returns a list of 1 4 vectors containing the cell origin center and as many basis vectors as exist i e ox oy oz ax ay az bx by bz cx cy cz It is more efficient to set the wrapping mode than to do periodic image calculations in Tcl getmass Returns the mass of the current atom getcharge Returns the charge of the current atom getid Returns the 1 based ID of the current atom addforce lt fx gt lt fy gt lt fz gt Adds the specified force to the current atom for this step addenergy lt energy gt Adds potential energy to the BOUNDARY column of NAMD output As an example these spherical boundary condition forces sphericalBC on sphericalBCcenter 0 0 0 0 0 0 sphericalBCri 48 sphericalBCk1 10 sphericalBCexp1 2 Are replicated in the following scrip
303. ten useful to reduce the great number of degrees of freedom of a into a few parameters which can be either analyzed individually or manipulated in order to alter the dynamics in a controlled manner These have been called order parameters collective variables surrogate reaction coordinates and many other terms In this section the term collective variable shortened to colvar is used and it indicates any differentiable function of atomic Cartesian coordinates x with 7 between 1 and N the total number of atoms E t wilt ej t e t LSij k SN 35 The colvars module in NAMD may be used in both MD simulation and energy minimization runs except free energy methods It offers several features e define an arbitrary number of colvars and perform a multidimensional analysis or biased simulation by accessing any subset of colvars independently from the rest see 10 1 e combine different functions of Cartesian coordinates herein termed colvar components into a colvar defined as a polynomial of several such components thereby implementing new func tional forms at runtime periodic multidimensional and symmetric components are handled transparently see 10 2 2 e calculate potentials of mean force PMFs for any set of colvars using different sampling methods currently implemented are the Adaptive Biasing Force ABF method see 10 3 1 metadynamics see 10 3 2 Steered Molecular Dynamic
304. tepping system alters the balance between bonded and non bonded forces from every timestep to an average balance over two steps the calculated pressure on even and odd steps will be different The PRESSAVG and GPRESSAVG fields provide the average over the non printed intermediate steps If you 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 V
305. ter 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 LJcorrection lt Apply long range corrections to the system energy and virial to account for neglected vdW forces gt Acceptable Values yes or no Default Value no Description Apply an analytical correction to the reported vdW energy and virial that is equal to the amount lost due to switching and cutoff of the LJ potential The correction will use the average of vdW parameters for all particles in the system and assume a constant homogeneous distribution of particles beyond the switching distance See 56 for details the equations used in the NAMD implementation are slightly different due to the use of a different switching function Periodic boundary conditions are required to make use of tail corrections LJcorrection as implemented is inconsistent with vdwForceSwitching 5 2 4 PME parameters PME stands for Particle Mesh Ewald and is an efficient full electrostatics method for use with periodic boundary conditions None of the parameters should affect energy conservation although they may affect the accuracy of the results and momentum conservation e PME lt Use particle mesh Ewald for electrostatics gt Acceptable Values yes or no Default V
306. teractions are fully enabled for exnihilated particles For an exnihilated particle vdW interactions are fully decoupled at A 0 The coupling of vdW interactions to the simulation is then increased with increasing values of A such that at values of A greater than or equal to alchVdwLambdaEnd the vdW interactions of the exnihilated particle are fully coupled to the simulation 148 For an annihilated particle vdW interactions are completely coupled to the simulation at A 0 This coupling linearly decreases for A values between 1 0 and 1 alchVdwLambdaEnd For A values greater than or equal to 1 alchVdwLambdaEnd vdW interactions of the annihilated particle are fully decoupled from the simulation e alchDecouple lt Disable scaling of nonbonded interactions within alchemical partitions gt Acceptable Values on or off Default Value off Description With alchDecouple set to on only nonbonded interactions of perturbed incoming and outgoing atoms with their environment are scaled while interactions within the subset of perturbed atoms are preserved On the contrary if alchDecouple is set to off interactions within the perturbed subset of atoms are also scaled and contribute to the cumulative free energy In most calculations intramolecular annihilation free energies are not particularly informative and decoupling ought to be preferred Under certain circumstances it may however be desirable to scale intramolecular interactions provi
307. ters of the colvars ABF also depends on parameters from collective variables to define the grid on which free energy gradients are computed In the direction of each colvar the grid ranges from lowerBoundary to upperBoundary and the bin width grid spacing is set by the width parameter Output files The ABF bias produces the following files all in multicolumn ASCII format e lt outputName gt grad current estimate of the free energy gradient grid in multicolumn e lt outputName gt count total number of samples collected on the same grid e lt outputName gt pmf only for one dimensional calculations integrated free energy profile or PMF If several ABF biases are defined concurrently their name is inserted to produce unique filenames for output as in lt outputName gt abf1 grad This should not be done routinely and could lead to meaningless results only do it if you know what you are doing If the colvar space has been partitioned into sections windows in which independent ABF sim ulations have been run the resulting data can be merged using the inputPrefix option described above a NAMD run of 0 steps is enough Reconstructing a multidimensional free energy surface If a one dimensional calculation is performed the estimated free energy gradient is automatically integrated and a potential of mean force is written under the file name lt outputName gt pmf in a plain text format that can be read by most data plotting
308. to allow simulated annealing protocols within a single config file The useGroupPressure useFlexibleCell useConstantArea useConstantRatio LangevinPis ton LangevinPistonTarget LangevinPistonPeriod LangevinPistonDecay LangevinPiston Temp SurfaceTensionTarget BerendsenPressure BerendsenPressureTarget BerendsenPres sureCompressibility and BerendsenPressureRelaxationTime parameters may be changed to 15 allow pressure equilibration The fixedAtoms constraintScaling and nonbondedScaling pa rameters may be changed to preserve macromolecular conformation during minimization and equilibration fixedAtoms may only be disabled and requires that fixedAtomsForces is en abled to do this The consForceScaling parameter may be changed to vary steering forces or to implement a time varying electric field that affects specific atoms The eField eFieldFreq and eFieldPhase parameters may be changed to implement at time varying electric field that affects all atoms The alchLambda and alchLambda2 parameters may be changed during alchemical free energy runs e The checkpoint and revert commands no arguments allow a scripted simulation to save and restore to a prior state e The exit command writes output files and exits cleanly e The abort command concatenates its arguments into an error message and exits immedi ately without writing output files e The numPes numNodes and numPhysicalNodes command
309. trostatics 6 1 3 Generalized Born Equations In a GB simulation the total electrostatic force on an atom 7 is the net Coulomb force on atom i from nearby atoms minus the GB force on atom i also caused by nearby atoms F poole pee 59 Forces are contributed by other nearby atoms within a cutoff The GB force on atom i is the derivative of the total GB energy with respect to relative atom distances rij po _ gt Ei 8 g gt 2 J where the partial derivatives are included since the Born radius a is a function of all relative atom distances The total GB energy of the system is DR E 11 2 i j gt i EFP d k E 2 Oar dry Ori OnG da OESB do DEF 0a drij l da drij Ori fji 9 Pi 10 where ESP is the Born radius dependent self energy of atom i and the GB energy between atoms i and j is given by EOP Sapp ge 12 fij The dielectric term 60 is 1 P D exp rta 13 Ep Es and the GB function 61 is r2 2 Fij ri 0505 exp e 14 As the Born radii of atoms i and j decrease increasing screening the effective distance between the atoms fij increases The implicit solvent implemented in NAMD is the model of Onufriev Bashford and Case 49 50 which calculates the Born radius as 1 Qk A tanh dv By vo 15 PkO where Uk Pko ye Hy 16 i Hj is the piecewise descreening function 50 28 55 the seven piecewise
310. ts 500 firstTimestep ts run 0 171 coorfile close 172 15 Translation between NAMD and X PLOR configuration pa rameters NAMD was designed to provide many of the same molecular dynamics functions that X PLOR provides As such there are many similarities between the types of parameters that must be passed to both X PLOR and NAMD This section describes relations between similar NAMD and X PLOR parameters e NAMD Parameter cutoff X PLOR Parameter CTOFNB When full electrostatics are not in use within NAMD these parameters have exactly the same meaning the distance at which electrostatic and van der Waals forces are truncated When full electrostatics are in use within NAMD the meaning is still very similar The van der Waals force is still truncated at the specified distance and the electrostatic force is still computed at every timestep for interactions within the specified distance However the NAMD integration uses multiple time stepping to compute electrostatic force interactions beyond this distance every stepspercycle timesteps e NAMD Parameter vdwswitchdist X PLOR Parameter CTONNB Distance at which the van der Waals switching function becomes active e NAMD Parameter pairlistdist X PLOR Parameter CUTNb Distance within which interaction pairs will be included in pairlist e NAMD Parameter 1 4scaling X PLOR Parameter E14Fac Scaling factor for 1 4 pair electrostatic interactions e NAMD Parameter diel
311. ture 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 7 4 5 Lowe Andersen dynamics parameters NAMD can perform Lowe Andersen dynamics a variation of Andersen dynamics whereby the radial relative velocities of atom pairs are randomly modified based on a thermal distribution The Lowe Andersen thermostat is Galilean invariant therefore conserving momentum and is thus 75 independent of absolute atom velocities Forces are applied only between non bonded non hydrogen pairs of atoms When using rigid bonds forces are applied to the center of mass of hydrogen groups The implementation is based on Koopman and Lowe 38 e loweAndersen lt use Lowe Andersen dynamics gt Acceptable Values on or off Default Value off Description Specifies whether or not Lowe Andersen dynamics are active If set to on then the parameter loweAndersenTemp must be set and the parameters loweAndersenCutoff and loweAndersenRate can optionally be set e loweAndersenTemp lt temperature for Lowe Andersen calculations K gt Acceptable Values positive decimal Description Temperature of the distribution used to set radial relative velocities This
312. ucive to numerical instabilities from molec ular dynamics simulations often coined as end point catastrophes These scenarios are prone to occur when A becomes close to 0 or 1 and incoming atoms instantly appear where other parti cles are already present which results in a virtually infinite potential as the interatomic distance tends towards 0 Such end point catastrophes can be profitably circumvented by introducing a so called soft core potential 5 43 aimed at a gradual scaling of the short range nonbonded interactions of incoming atoms with their environment as shown in Equation 55 What is really being modified is the value of a coupling parameter ALJ or elec that scales the interactions e if set to 0 the latter are off if set to 1 they are on in lieu of the actual value of A provided by the user Rin 2 6 Rmin 2 3 V io A ij ij ij e ec n 55 NB rij LJEij 0 1 wa gt 6 1 5 pe a It is also worth noting that the free energy calculation does not alter intermolecular bonded potentials e g bond stretch valence angle deformation and torsions in the course of the simulation In calculations targeted at the estimation of free energy differences between two states characterized by distinct environments e g a ligand bound to a protein in the first simulation and solvated in water in the second as is the case for most free energy calculations that make use of a thermody
313. ularly adapted for performing free energy cal culations that split the A reaction path into a number of non physical intermediate states or windows Separate simulations can be started for each window Alternatively the TCL scripting ability of NAMD can be employed advantageously to perform the complete simulation in a single run An example making use of such a script is supplied at the end of this section The following keywords can be used to run alchemical free energy calculations whether FEP or TI e alch lt Is an alchemical transformation to be performed gt Acceptable Values on or off Default Value off Description Turns on alchemical transformation methods in NAMD e alchType lt Which method is to be employed for the alchemical transformation gt Acceptable Values fep or ti Default Value ti Description Turns on Hamiltonian scaling and ensemble averaging for alchemical FEP or TI e alchLambda lt Current value of the coupling parameter gt Acceptable Values positive decimal between 0 0 and 1 0 Description The coupling parameter value determining the progress of the perturbation for FEP or TI e alchLambda2 lt Forward projected value of the coupling parameter gt Acceptable Values positive decimal between 0 0 and 1 0 Description The lambda2 value corresponds to the coupling parameter to be used for sam pling in the next window The free energy difference between alchLambda2 and alchLambda is calculated
314. up 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 2 168 14 2 Pressure profile calculations NAMD supports the calculation of lateral pressure profiles as a function of the z coordinate in the system The algorithm is based on that of Lindahl and Edholm JCP 2000 with modifications to enable Ewald sums based on Sonne et al JCP 122 2005 The simulation space is partitioned into slabs and half the virial due to the interaction between two particles is assigned to each of the slabs containing the particles This amounts to employing the Harasima contour rather than the Irving Kirkwood contour as was done in NAMD 2 5 The diagonal components of the pressure tensor for each slab averaged over all timesteps since the previous output are recorded in the NAMD output file The units of pressure are the same as in the regular NAMD pressure output i e bar The total virial contains contributions from up to four components kinetic energy bonded interactions nonbonded interactions and an Ewald sum All but the Ewald sums are computed online during a normal simulation run this is a change from NAMD 2 5 when nonbonded contri butions to the Ewald sum were always computed offline If the simulations are performed using PM
315. up which only intervenes through its center center of mass or geometric center in the force measurement In the latter case the contributions of the two atoms to the left hand side of equation 49 cancel out For example all atoms of a rigid TIP3P water molecule can safely be included in an atom group used in a distance component 132 Parameters for ABF The following parameters can be set in the ABF configuration block in addition to generic bias parameters such as colvars e fullSamples lt ABF Number 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 e hideJacobian lt ABF Remove geometric entropy term from calculated free energy gradi ent gt Acceptable Values boolean Default Value no Description In a few special cases most notably distance based variables an alternate definition of the potential of mean force is traditionally used which excludes the Jacobian term describing the effect of geometric entropy on the distribution of the variable This re sults for example in particle particle potentials of mean force being flat at large separations Setting this parameter to yes causes the output
316. using which water model gt Acceptable Values tip3 tip4 swm4 Default Value tip3 Description Specifies the water model to be used When using the TIP3P water model the ordering of atoms within each TIP3P water molecule must be oxygen hydrogen hydro gen When using the TIP4P water model the ordering of atoms within each TIP4P water molecule must be oxygen hydrogen hydrogen lone pair When using the SWM4 NDP water model the ordering of atoms within each SWM4 NDP water molecule must be oxygen Drude particle lone pair hydrogen hydrogen Alternative orderings will fail 5 4 Drude polarizable force field The Drude oscillator model represents induced electronic polarization by introducing an auxiliary particle attached to each polarizable atom via a harmonic spring The advantage with the Drude model is that it preserves the simple particle particle Coulomb electrostatic interaction employed in nonpolarizable force fields thus its implementation in NAMD is more straightforward than alter native models for polarization NAMD performs the integration of Drude oscillators by employing a novel dual Langevin thermostat to freeze the Drude oscillators while maintaining the warm de grees of freedom at the desired temperature 34 Use of the Langevin thermostat enables better parallel scalability than the earlier reported implementation which made use of a dual Nos Hoover thermostat acting on and within each nucleus Drude pair 41 Performan
317. ut 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 the 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 2 2 Electrostatic interactions The handling of electrostatics is slightly more complicated due to the incorporation of multiple timestepping for full electrostatic interactions There are two cases to consider one where full electrostatics is employed and the other where electrostatics are truncated at a given distance First let us consider the latter case where electrostatics are truncated at the cutoff distance Using this scheme all electrostatic interactions beyond a specified distance are ignored or assumed to be zero If switching is set to on rather than having a discontinuity in the potential at the cutoff distance a shifting function is applied to the electrostatic potential as shown in Figure 2 As this figure shows the shifting function shifts the entire potential curve so that the curve intersects the x axis at the cutoff distance This shifting function is based on the shifting function used by X PLOR Next consider the case where full electrostatics are calculated In this case the electrostatic interactions are not trunc
318. ware 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 Insti tute available free of charge for non commercial use by individuals academic or research insti tutions and corporations for in house business purposes only upon completion and submission of the online registration form presented when attempting to download NAMD at the web site http www ks uiuc edu Research namd Commercial use of the NAMD software or derivative works based thereon REQUIRES A COMMERCIAL LICENSE Commercial use includes 1 integration of all or part of the Software into a product for sale lease or license by or on behalf of Licensee to third parties or 2 distribution of the Software to third parties that need it to commercialize product sold or licensed by or on behalf of Licensee The University of Illinois will negotiate commercial use licenses for NAMD upon request These requests can be directed to namd ks uiuc edu Online Download Registration Requirements In completing the online registration form presented before downloading individuals may register in their own name or with their institutional or corporate affiliations Registration information must include name title and e mail of a person with signature authority to authorize and commit the individuals academic or r
319. 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 7 1 2 Spherical harmonic boundary conditions NAMD provides spherical harmonic boundary conditions These boundary conditions can consist of a single potential or a combination of two potentials The following parameters are used to define these boundary conditions e sphericalBC lt use spherical boundary conditions gt Acceptable Values on or off Default Value off Description Specifies whether or not spherical boundary conditions are to be applied to the system If set to on then sphericalBCCenter sphericalBCri and sphericalBCk1 must be defined and sphericalBCexp1 sphericalBCr2 sphericalBCk2 and sphericalBCexp2 can optionally be defined e sphericalBCCenter lt center of sphere A gt Acceptable Values position Description Location around which sphere is centered e sphericalBCri lt radius for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect This distance is a radius from the center e sphericalBCk1 lt force constant for first potential gt Acceptable Values non zero decimal 66 Description
320. y step For long simulations the amount of output generated by NAMD can be greatly reduced by outputting the energies only occasionally e mergeCrossterms lt add crossterm energy to dihedral gt Acceptable Values yes or no Default Value yes Description If crossterm or CMAP terms are present in the potential the energy is added to the dihedral energy to avoid altering the energy output format Disable this feature to add a separate CROSS field to the output e outputMomenta lt timesteps between momentum output gt Acceptable Values nonnegative integer Default Value 0 Description The number of timesteps between each momentum output of NAMD If specified and nonzero linear and angular momenta will be output to stdout e outputPressure lt timesteps between pressure output gt Acceptable Values nonnegative integer Default Value 0 Description The number of timesteps between each pressure output of NAMD If specified and nonzero atomic and group pressure tensors will be output to stdout e outputTiming lt timesteps between timing output gt Acceptable Values nonnegative integer Default Value the greater of firstLdbStep or 10x outputEnergies 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 23 3 3 AMBER force field parameters
321. ymin zmin min break foreach xmax ymax zmax max break set xmin expr xmin 10 set ymin expr ymin 10 set zmin expr zmin 10 set xmax expr xmax 10 set ymax expr ymax 10 set zmax expr zmax 10 Center the water on the protein Also update the coordinates held by psfgen set wat atomselect top segid QQQ wat moveby vecsub measure center protein measure center wat foreach atom wat get segid resid name x y z foreach segid resid name x y z atom break coord segid resid name list x y z Select waters that we don t want in the final structure 34 set outsidebox atomselect top segid QQQ and x lt xmin or y lt ymin or z lt zmin or x gt xmax or y gt ymax or z gt xmax set overlap atomselect top segid QQQ and within 2 4 of not segid QQQ Get a list of all the residues that are in the two selections and 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 y
322. ystem has deposited hills across the whole free energy landscape In this situation Vineta amp is a good approximant of the free energy A and the only dependence on the specific conformational history 6t 26t is by an irrelevant additive constant A Vmneta K 53 Provided that the set of collective variables fully describes the relevant degrees of freedom the accuracy of the reconstructed profile is a function of the ratio between W and t 11 For the optimal choice of d and D the diffusion constant of the variable see reference 11 As a rule of thumb the very upper limit for the ratio W t is given by kgT Tg where TE is the longest among s correlation times In the most typical conditions to achieve a good statistical convergence the user would prefer to keep W t much smaller than kT T Given A the extension of the free energy profile along the colvar and A A amp the highest free energy that needs to be sampled e g that of a transition state the upper bound for the required simulation time is of the order of Ns A A W2d multiples of t When several colvars are used the upper bound amounts to Ns 1 x Ns 2 x x NslEn X t In metadynamics runs performed with this module the parameter g for each hill eq 52 is chosen as approximately half the width of the corresponding colvar while all the other parameters must be p

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