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1. yi ef T zi zres BS Gradient for stretch restraint E K5 2 di dref di z2 21 o Y 22 21 V E Ky di dres V di for atom 2 moving and atom 1 fixed 0 2 0 4 0 6 0 8 1 0 V d 1 2 22 21 10 22 ay 2 we 21 208 m 22 2 vid x2 1 y2 y1 F 22 21 E d V E Kr di dref di x2 z1 i y2 3 J 22 21 E Gradient for bend restraint E Ky 2 0 06 45 Atoms at positions A B C distances A to B c A toC b BtoC a 0 cos u cos a c b 2ac V E Ky 0 a Oreg E V 0 V 8 V u for atom A moving atoms B amp C fixed distances b and c change V u b ac V b a 2c 1 2a amp 2ac V c V b v4 zc Y ya yc F 24 zc E b V c xa zB T ya yB Y za zB E c 59 for atom B moving atoms A amp C fixed distances a and c change V u 1 2c 2a b 2a c V a a 2c 1 2a b 2ac V c V a xp zo yB vc zB zc a V c zn 24 Y yp 44 3 zB za K c for atom C moving atoms A amp B fixed distances a and b o V u b ac V b c 2a 1 2c b 2a V a V b sc za yc ya j zc 24 K fo V a zc 28 1 yc v8 3 zc
2. 63 7 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 timestep 0 5 numsteps 10000 cwd scratch Specify a working directory structure alanin psf parameters alanin params coordinates alanin pdb exclude scaledi 4 1 4scaling 0 4 outputname output margin 1 0 stepspercycle 10 temperature 300 0 switching on switchdist 7 0 cutoff 8 0 pairlistdist 9 0 64 This file is again for alanin but shows a slightly more complicated configuration A coordinate trajectory file and a set of restart files are produced every ten timesteps Langevin dynamics are also active in this configuration timestep numsteps structure parameters coordinates exclude 1 4scaling outputname margin stepspercycle temperature switching switchdist cutoff pairlistdist DCDfile DCDfreq restartname restartfreq langevin langevinTemp langevinCol 0 5 10000 alanin psf alanin params alanin pdb scaledi 4 0 4 output 1 0 10 300 0 ON ooo alanin dcd 10 alanin restart 10 on 300 0 65 This file shows another simple configuration file for alanin but this time with full electrostatics using DPMTA timestep numsteps cwd structure parameters coordinates exclude 1 4scaling outputname margin stepsperc
3. zn K a Gradient for dihedral angle restraint E Eo 2 1 COS xi x Xref Atoms at positions A B C D A EN CDxCBy B x B BEES NEQU l cB CBI BC Bal ae Nw sin v zx CDxCB x BCxBA CB a i Az BCxBA TEB V E Eo 2 sin xi Xref VO V xi zu VQ CDxCB yp yc ze zo zp 2c ye yc zp 2c tB zc p to Mer 20 3 tp zc ys yc up yo Mer zc k pit p2j psk gt bog BC x BA yo ys za 28 sc 28 yA ym t zc zB z4 ZB xc zB z4 zB rc vB yA yB yc YB TA 2B pat psj p6k u papai Fpops pape VPi tP3 3 y DG D5 DG _ prV ps O 5 p3 V po MT TAERA S o oa 1P4 2 E 1 2 03 pi r 2p4 V p4 2ps V ps 2p6 V po rapto 1 2 pj p3 p3 2p1 Vio 2p2 V p2 2p3 V p3 for atom A muno atoms B C 8 D fixed V p1 0 0 i 0 0 j 0 0 amp V p2 oes 0 0 7 0 0 amp V ps 0 0 T 0 0 7 0 0 amp V pa 00 zB 2c0 j yo yp F V ps 20 28 1 0 0 7 zs zc k Vips ue y0 xo zg j 0 0 k 60 for atom B moving atoms A C amp D fixed V pi 0 0 zc 25 i yD yc k V p2 2D 2c 1 0 0 9 F zc ap k V ps wc wp ic zp zc j 0
4. NAMD User s Guide Version 2 1 M Bhandarkar R Brunner A Dalke J Gullingsrud A Gursoy W Humphrey D Hurwitz N Krawetz M Nelson J Phillips A Shinozaki October 7 1999 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 1 Authors M Bhandarkar R Brunner A Dalke J Gullingsrud A Gursoy W Humphrey D Hurwitz N Krawetz M Nelson J Phillips A Shinozaki Theoretical Biophysics Group Beckman Institute University of Illinois c 1995 99 The Board of Trustees of the University of Illinois All Rights Reserved NAMD Molecular Dynamics Software Non Exclusive Non Commercial Use License Introduction The University of Illinois at Urbana Champaign has created its molecular dynamics software NAMD developed by the Theoretical Biophysics Group TBG at Illinois Beckman Institute available free of charge for non commercial use by individuals academic or research institutions and corporations for in house business purposes only upon completion and submission of the following registration form Co
5. Description Location around which cylinder is centered cylindricalBCAxis lt axis of cylinder A gt Acceptable Values x y or z Description Axis along which cylinder is aligned cylindricalBCri lt radius for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect along the non axis plane of the cylinder cylindricalBC11 lt distance along cylinder axis for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect along the cylinder axis cylindricalBCk1 lt force constant for first potential gt Acceptable Values non zero decimal Description Force constant for the first harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center cylindricalBCexp1 lt exponent for first potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for first boundary potential The only likely values to use are 2 and 4 40 e 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 spericalBC
6. 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 4 2 Full electrostatic integration To further reduce the cost of computing full electrostatics NAMD uses a multiple timestepping integration scheme In this scheme the total force acting on each atom is broken into two pieces a quickly varying local component and a slower long range component The local force component is defined in terms of a splitting function The local force component consists of all bonded and van der Waals interactions as well as that portion of electrostatic interactions for pairs that are separated by less than the local interaction distance determined by the splitting function The long range component consists only of electrostatic interactions outside of the local interaction distance Since the long range forces are slowly varying they are not evaluated every timestep Instead they are evaluated every k timesteps and each set of k timesteps is referred to as a cycle The value of k is specified by the NAMD parameter stepspercycle 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 o
7. This work is supported by grants from the National Science Foundation BIR 9318159 and the National Institute of Health PHS 5 P41 RR05969 04 The authors would particularly like to thank the members of the Theoretical Biophysics Group past and present who have helped tremendously in making suggestions pushing for new features and testing bug ridden code 14 2 Getting Started 2 1 What is needed Before running NAMD explained in section 8 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 We strongly recommend that you have access to either CHARMM or X PLOR either of which is capable of generating both the PSF and PDB files NAMD currently provides no automatic method of generating these 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 simulati
8. specified by cutoff The main option that effects van der Waals interactions is the switching parameter With this option set to on a smooth switching function will be used to truncate the van der Waals potential energy smoothly at the cutoff distance A graph of the van der Waals potential with this switching function is shown in Figure 1 If switching is set to off the van der Waals energy is just abruptly truncated at the cutoff distance so that energy may not be conserved switchdist cutoff paar eae mae AAA b x energy T I I I I I distance Figure 1 Graph of van der Waals potential with and without the application of the switching function With the switching function active the potential is smoothly reduced to 0 at the cutoff distance Without the switching function there is a discontinuity where the potential is truncated The details of the switching function are given in the NAMD Programmer s Guide The switch ing 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 4 1 2 Non bonded electrostatic interactions The handling of electrostatics is slightly more complicated due to the incorporation of multiple timestepping for full electrostatic int
9. to allow you to view and interactively steer your simulation NAMD will wait for VMD to connect on startup Faster particle mesh Ewald If for some reason you wish to use the slower DPME implementation of the particle mesh Ewald method add useDPME yes If you set cellOrigin to something other than 0 0 0 the energy may differ slightly between the old and new implementations For even better performance get the NAMD source code and compile with FFTW 1 2 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 7 In order to conduct MD simulations various computer programs have been developed including X PLOR 5 and CHARMM 4 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 th
10. Hello World e atomid lt molname gt lt resid gt lt atomname gt Determines atomid of an atom from its molecule residue and name For example atomid br 2 N e addatom lt atomid gt Request coordinates of this atom for next force evaluation Request remains in effect until reconfig is called For example addatom 4 or addatom atomid br 2 N e addgroup lt atomid list gt Request center of mass coordinates of this group for next force evaluation Returns a group ID which is of the form gN where N is a small integer This group ID may then be used to find coordinates and apply forces just like a regular atom ID Aggregate forces may then be applied to the group as whole Request remains in effect until reconfig is called For example set groupid addgroup 14 10 12 e reconfig Signals that new atoms are being requested addatom and addgroup calls during calcforces will be ignored unless reconfig is called Old configuration is replaced by new configuration reconfig should only be called from within the calcforces procedure 51 e loadcoords lt varname gt Loads requested atom and group coordinates in A into a local array loadcoords should only be called from within the calcforces procedure For example loadcoords p and print p 4 e 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 pro
11. This amortizes the cost of computing the electrostatic forces over several timesteps A smooth splitting function is used to separate a quickly varying short range portion of the electrostatic interaction from a more slowly varying long range component It is also possible to employ an intermediate timestep for the short range non bonded interactions performing only bonded interactions every timestep e Input and Output Compatibility The input and output file formats used by NAMD are identical to those used by CHARMM 10 and X PLOR Input formats include coordinate files in PDB format 2 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 Rigid bonds to hydrogen Harmonic restraints Spher
12. This will insure energy conservation NAMD 2 X eliminated the explicit use of pairlists in order to reduce memory usage in light of equally efficient distance testing algorithms Specifically it was realized that building a pairlist on top of the existing spatial decomposition was only marginally more efficient than actually testing atom distances at every timestep given efficient methods for dealing with nonbonded exclusions The pairlistdist parameter now serves the same function but is instead 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 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 24 pairlist distance cutoff gt lt Figure 4 Depiction of the difference between the cutoff distance and the pair list distance
13. 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 Description Force constant for the first harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center e sphericalBCexp1 lt exponent for first potential gt Acceptable Values positive even integer 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 di
14. 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 lists basic simulation options Section 5 lists additional simulation options Section 6 provides hints for X PLOR users Section 7 provides sample configuration files Section 8 gives details on running NAMD Section 9 gives details on installing NAMD We have attempted to make this document and the NAMD Programmer s Guide both complete and easy to understand and to make NAMD itself easy to install and run Please take a moment to help us improve the documentation and the code by filling out the users survey at the end of this section 1 1 New features in version 2 1 Mollified impulse method MOLLY 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 rigid Bonds all with MOLLY makes no sense since the degrees of freedom which MOLLY protects from resonance are already frozen Non orthogonal periodic cells The parameters cellBasisVector 123 and cellOrigin have not changed but the basis vectors may now be in any direction Interactive molecular dynamics NAMD now works directly with VMD http www ks uiuc edu Research vmd
15. find 0 All 0 values that exceed 0 2 are ignored The distribution of 0 values is given by 02 xp 75 7 After the angles y and are calculated the new direction is found by constructing a right orthonormal system of coordinates with fig the initial direction specified by SMDDir in the config uration file being the z direction The other two vectors d and b orthogonal to riy and to each other are found by first producing fio x 0 1 1 or d o x 1 1 1 in the case when o is p 0 e gay 27 collinear to 0 1 1 normalizing d and finally producing b rig X a Then the new direction is given by a Tinew Acosysind bsingsin0 rigcos0 8 Resetting the applied force Sometimes especially when a small enough k is employed the movement of the restrained atom proceeds in steps resulting in a fast movement of the atom over a short period of time When this happens it may be desirable to reset reduce the applied force Resetting of the force to a specified value Fmin SMDFmin should happen when the average velocity of atom movement v max over a given period of time Tmax SMDVmaxTave exceeds the specified maximum allowed velocity Umar SMDVmax in the direction of reference position movement 7 The average velocity is calculated similarly to Eq 5 and in the case when v maz is larger than Umax the reference position is reset according to Eq 6 The time stamp to is set to current time Output NAMD pr
16. for most applications 4 3 5 PME parameters PME stands for Particle Mesh Ewald and is an efficient full electrostatics method for use with periodic boundary conditions None of the parameters should affect energy conservation although they may affect the accuracy of the results and momentum conservation e PME lt Use particle mesh Ewald for electrostatics gt Acceptable Values yes or no Default Value no Description Turns on particle mesh Ewald e PMETolerance lt PME direct space tolerance gt Acceptable Values positive decimal 30 Default Value 10 9 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 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 e PMEGridSizeX lt PME grid 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 e PMEGridSizeY lt PME grid in y dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeY should have only small integer factors 2 3 and 5 e PMEGridSizeZ
17. in degrees of the cone with the axis along the initial direction of the reference position movement SMDDir The new direction will come from the vertex of the cone and will lie within the cone This angle is twice the angle between the cone s axis and any line going through the cone s vertex on the cone s surface Omitting this parameter will lead to choosing a direction without any restrictions all directions are possible 49 e SMDChDirMethod lt method to use when choosing a new direction gt Acceptable Values gaussian uniform Default Value uniform Description The method to choose the angle between the new direction and the initial direction of the reference position movement When gaussian is specified it is recommended to set the variance of the distribution with SMDGaussW e SMDGaussW lt variance of the gaussian distribution used to choose new directions gt Acceptable Values positive real Default Value 360 Description Variance of the gaussian distribution in degrees used for choosing the angle between the new direction and the initial direction of the reference position movement e SMDChForce lt is resetting force SMD option active gt Acceptable Values on off Default Value off Description If turned on this option allows to reset the reference position so that the applied force becomes SMDFmin when the average velocity of the restrained atom in the direction of the reference position movement is larger than a gi
18. kf KF ref X Y Z dist 2x ATOM kf KF ref D angle 3x ATOM kf KF ref A dihe 4xATOM barr B ref A Bound Specifications not coupled to pmf calculations posi bound ATOM kf KF low X Y Z D or hi X Y Z D dist bound 2x ATOM kf KF low D or hi D angle bound 3x ATOM kf KF low A or hi A dihe bound 4x ATOM gap E low A0 hi A1 delta A2 Forcing Restraint Specifications coupled to pmf calculations posipmf ATOM dist pnf 2x ATOM angle pmf 3x ATOM dihe pmf 4x ATOM kf KF low X0 YO Z0 hi X1 Y1 Z1 kf KF low D0 hi D1 kf KF low A0 hi A1 barr B low A0 hi A1 Units Input item Units E B kcal mol X Y Z D A degrees Ky kcal mol or kcal mol rad 5 7 4 Options for ATOM Specification The designation ATOM above stands for one of the following forms A single atom segname resnum atomname Example insulin 10 ca All atoms of a single residue segname resnum Example insulin 10 A list of atoms 55 group segname resnum atomname segname resnum atomname Example group insulin 10 ca insulin 10 cb insulin 11 cg All atoms in a list of residues group segname resnum segname resnum Example group insulin 10 insulin 12 insulin 14 All atoms in a range of residues group segname resnum to segname resnum Example group insulin 10 to insulin 12 One or more atomnames
19. lower and upper bound Torsional bounds always are defined in pairs 5 7 2 Free Energy Calculations Conformational forcing Potential of mean force In conformational forcing calculations structural parameters such as atomic positions inter atomic distances and dihedral angles are forced to change by application of changing restraint potentials For example the distance between two atoms can be restrained by a potential to a mean distance that is varied during the calculation The free energy change or potential of mean force pmf for the process can be estimated during the simulation The potential is made to depend on a coupling parameter A whose value changes during the simulation In potential of mean force calculations the reference value of the restraint potential depends on A Alternately the force constant for the restraint potential may change in proportion to the coupling parameter Such a calculation gives the value of a restraint free energy i e the free energy change of the system due to imposition of the restraint potential Methods for computing the free energy With conformational forcing or with molecular transformation calculations one obtains a free energy difference for a process that is forced on the system by changing the potential energy function that determines the dynamics of the system One always makes the changing potential depend on a coupling parameter A By convention A can have values only in the ran
20. lt PME grid in z dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeZ should have only small integer factors 2 3 and 5 e useDPME lt Use old DPME code gt Acceptable Values yes or no Default Value no Description Switches to old DPME implementation of particle mesh Ewald The new code is faster and allows non orthogonal cells so you probably just want to leave this option turned off If you set cell0rigin to something other than 0 0 0 the energy may differ slightly between the old and new implementations 4 3 6 Full direct parameters The direct computation of electrostatics is not intended to be used during real calculations but rather as a testing or comparison measure Because of the O N computational complexity for performing direct calculations this is much slower than using DPMTA or PME to compute full electrostatics for large systems In the case of periodic boundary conditions the nearest image convention is used rather than a full 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 31 4 3 7 Multiple timestep parameters One of the areas of current research being studied using NAMD is the exploration of better methods for performing multiple t
21. 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 dielectric lt dielectric constant for system gt Acceptable Values decimal gt 1 0 Default Value 1 0 Description Dielectric constant for the system A value of 1 0 implies no modification of the electrostatic interactions Any larger value will lessen the electrostatic forces acting in the system 1 4scaling lt scaling factor for 1 4 interactions gt Acceptable Values 0 lt decimal lt 1 Default Value 1 0 Description Scaling factor for 1 4 interactions This factor is only used when the exclude parameter is set to scaled1 4 In this case this factor is used to modify the electrostatic inter actions between 1 4 atom pairs If the exclude parameter is set to anything but scaledi 4 this parameter has no effect regardless of its value seed random number seed Acceptable Values positive integer 28 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 p
22. perturbation script is described below The following sections describe the format of the free energy perturbation script 5 7 1 User Supplied Conformational Restraints These restraints extend the scope of the available restraints beyond that provided by the harmonic position restraints Each restraint is imposed with a potential energy term whose form depends on the type of the restraint Fixed Restraints Position restraint 1 atom force constant Kp and reference position fref E Kp 2 Trefl Stretch restraint 2 atoms force constant Ky and reference distance dref 52 E Ky 2 di dyep Bend restraint 3 atoms force constant Kp and reference angle Oe E K 5 2 0 Ores Torsion restraint 4 atoms energy barrier Eo and reference angle Xref E Ep 2 1 COS xi Xref Forcing restraints Position restraint 1 atom force constant Kp and two reference positions rj and rj E K 2 r Frefl Pref ATT 1 A r Stretch restraint 2 atoms force constant K and two reference distances dy and d E K 7 2 d dref dref d 1 A do Bend restraint 3 atoms force constant Kp and two reference angles 09 and 01 E K5 2 9 Ores Ores A04 1 A 06 Torsion restraint 4 atoms energy barrier Eo and two reference angles xo and x1 E Ep 2 11 COS xi Xref Xref AX1 1 A xo The forcing restraints depend on the coupling parameter A
23. slow network 5 6 5 Tcl interface 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 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
24. the distance at which electrostatic and van der Waals forces are truncated When full electrostatics are in use within NAMD the meaning is still very similar The van der Waals force is still truncated at the specified distance and the electrostatic force is still computed at every timestep for interactions within the specified distance However the NAMD integration uses multiple time stepping to compute electrostatic force interactions beyond this distance every stepspercycle timesteps e NAMD Parameter vdwswitchdist X PLOR Parameter CTONNB Distance at which the van der Waals switching function becomes active e NAMD Parameter pairlistdist X PLOR Parameter CUTNb Distance within which interaction pairs will be included in pairlist e NAMD Parameter 1 4scaling X PLOR Parameter E14Fac Scaling factor for 1 4 pair electrostatic interactions e NAMD Parameter dielectric X PLOR Parameter EPS Dielectric constant e NAMD Parameter exclude X PLOR Parameter NBXMod Both parameters specify which atom pairs to exclude from non bonded interactions The ability to ignore explicit exclusions is not present within NAMD thus only positive values of NBXMod have NAMD equivalents These 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
25. the velocities in the system are periodically rescaled so that the entire system is set to the desired temperature The following parameters specify how often and to what temperature this rescaling is performed e rescaleFreq lt number of timesteps between temperature rescaling gt Acceptable Values positive integer Description The equilibration feature of NAMD is activated by specifying the number of timesteps between each temperature rescaling If this value is given then the rescaleTemp parameter must also be given to specify the target temperature e rescaleTemp lt temperature for equilibration K gt Acceptable Values positive decimal Description The temperature to which all velocities will be rescaled every rescaleFreq timesteps This parameter is valid only if rescaleFreq has been set 5 3 4 Temperature reassignment parameters NAMD allows equilibration of a system by means of temperature reassignment Using this method all of the velocities in the system are periodically reassigned so that the entire system is set to the desired temperature The following parameters specify how often and to what temperature this reassignment is performed e 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 reass
26. 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 62 NAMD Parameter switching X PLOR Parameter SHIFt VSWItch and TRUNcation Activating the NAMD option switching is equivalent to using the X PLOR options SHIFt and VSWItch Deactivating switching is equivalent to using the X PLOR option TRUNcation NAMD Parameter temperature X PLOR Parameter FIRSttemp Initial temperature for the system NAMD Parameter rescaleFreq X PLOR Parameter IEQFrq Number of timesteps between velocity rescaling NAMD Parameter rescaleTemp X PLOR Parameter FINAltemp Temperature to which velocities are rescaled NAMD Parameter restartname X PLOR Parameter SAVE Filename prefix for the restart files NAMD Parameter restartfreq X PLOR Parameter ISVFrq Number of timesteps between the generation of restart files NAMD Parameter DCDfile X PLOR Parameter TRAJectory Filename for the position trajectory file NAMD Parameter DCDfreq X PLOR Parameter NSAVC Number of timesteps between writing coordinates to the trajectory file NAMD Parameter velDCDfile X PLOR Parameter VELOcity Filename 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
27. v is calculated every timestep for the angle of rotation corresponding to the current timestep angle Qt where 2 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 Ro 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 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 syste
28. 0 k V p4 00 zc 24 3 ya yc k V ps 2a 2c t 0 0 7 ac wa k Vips wc yA i ta ac j 0 0 k Gradient for forcing position restraint E K5 2 lr Frefl Tref ATI 1 A T 2 2 2 1 2 dE dA Kyx ti Brey Yi Yref ey x 2 2 ay 71 2 1 2 la Tref F yi EZ Yref F E Zref 2 i Eres xo 21 2 yi Yref yo Ya 2 zi Zref 20 21 dE dA Ky x zi tres o 21 Yi Yref yo 91 zi Zref 20 21 Gradient for forcing stretch restraint E Ky 2 di dref dref Ad 1 A do dE dx Ky x d dref x do di Gradient for forcing bend restraint E K5 2 0 Ores Ore A0 1 A 0o dE dx Kr x 6 Oref x 00 01 Gradient for forcing dihedral restraint E Eo 2 1 cos xi Xref Xref AX1 1 A xo dE dA E0 2 x sin xi Xref X xo x1 61 6 Translation between NAMD and X PLOR configuration param eters NAMD was designed to provide many of the same molecular dynamics functions that X PLOR provides As such there are many similarities between the types of parameters that must be passed to both X PLOR and NAMD This section describes relations between similar NAMD and X PLOR parameters e NAMD Parameter cutoff X PLOR Parameter CTOFNB When full electrostatics are not in use within NAMD these parameters have exactly the same meaning
29. 5 15 16 17 17 17 17 17 17 17 17 19 22 22 22 22 24 25 26 26 26 27 29 30 31 32 5 3 2 Temperature coupling parameters 5 3 3 Temperature rescaling parameters 5 3 4 Temperature reassignment parameters 5 4 Boundary Conditions gt s sos ma sta som n aes d 2a Re UR eee ee eee 5 4 1 Spherical harmonic boundary conditions 5 4 2 Cylindrical harmonic boundary conditions 5 4 3 Periodic boundary conditions 99 Pressure Control 3 5 a 4 A A A E R ARD Ax a x TA t 5 5 1 Berendsen pressurebathcoupling 5 5 2 Nos Hoover Langevin piston pressure control 5 6 Applied Forces and Analysis 5 6 1 Moving Constraints 2r a RE E 5 6 2 Rotating Constraints 5 6 3 Steered Molecular Dynamics SMD 5 6 4 Interactive Molecular Dynamics IMD 5 6 5 Tbelinterfaee cg har Psd Bowe hes eee Ry God Eee SP A we RU 5 7 Free Energy of Conformational Change Calculations 5 7 1 User Supplied Conformational Restraints 5 7 2 Free Energy Calculations 5 7 3 Options for Conformational Restraints 5 7 4 Options for ATOM Specification 5 7 5 Options for Pot
30. D is a shared memory version and does not need any particular host program to launch NAMD Thus in order to run NAMD on Origin2000 we use the following command namd2 lt config file gt pN where Nis the number of processes we plan to use However note that depending on the load and the queuing strategy employed by the system some of the processes may be interleaved on some processors thus causing the performance to suffer Some installations of Origin2000 employ an external queuing facility to avoid this problem You are strongly encouraged to consult your local documentation for queuing facility used 8 2 Interactive modeling with MDScope Interactive molecular modeling can be performed using the MDScope environment MDScope consists of NAMD VMD a program for interactive visualization of biopolymers and MDComm a communications library for efficient network transfer of molecular dynamics information VMD allows the user to view intermediate results of the simulation being performed by NAMD while the simulation is still proceeding For more information regarding the installation or use of MDScope consult the VMD documentation 68 9 NAMD Availability and Installation NAMD is distributed freely for non profit use NAMD 2 1 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 instal
31. File formats 3 1 1 PDB files The PDB Protein Data Bank format is used to store coordinate or velocity data being input or output from NAMD This is the standard format for coordinate data for most other molecular dynamics programs as well including X PLOR and CHARMM A full description of this file for mat can be obtained via anonymous FTP from ftp pdb bnl gov in pub format desc ps Z or pub format desc txt 3 1 2 X PLOR format PSF files NAMD uses the same protein structure files that X PLOR does At this time the easiest way to generate these files is using X PLOR or CHARMM although it is possible to build them by hand CHARMM can generate an X PLOR format PSF file with the command write psf card xplor 3 13 CHARMM19 and CHARMM22 parameter files NAMD supports CHARMM19 and CHARMM22 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 5 3 1 4 DCD trajectory files NAMD produces DCD trajectory files in the same format as X PLOR and CHARMM The DCD files are single precision binary FORTRAN files so are transportable between computer architec tures They are not unfortunately transportable between big endian most workstations and little endian Intel architectures This same caveat applies to binary ve
32. LOR which is detailed in the X PLOR User s Manual 5 e tCouple lt perform temperature coupling gt Acceptable Values on or off Default Value off Description Specifies whether or not temperature coupling is active If set to on then the parameter tCoupleTemp must be set and the parameters tCoupleFile and tCoupleCol can optionally be set to control the behavior of this feature e tCoupleTemp lt temperature for heat bath K gt Acceptable Values positive decimal Description Temperature to which atoms affected by temperature coupling will be ad justed This temperature will be roughly maintained across the affected atoms through the addition of forces e tCoupleFile lt PDB file with tCouple parameters gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to use for the temperature coupling coefficient for each atom If this parameter is not specified then the PDB file specified by coordinates is used e tCoupleCol lt column of PDB from which to read coefficients gt Acceptable Values X Y Z 0 or B Default Value 0 37 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 5 3 3 Temperature rescaling parameters NAMD allows equilibration of a system by means of temperature rescaling Using this method all of
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34. Y 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 33 5 Additional Simulation Parameters 5 1 Constraints and Restraints 5 1 1 Harmonic constraint parameters The following describes the parameters for the harmonic constraints feature of NAMD Actually this feature should be referred to as harmonic restraints rather than constraints but for historical reasons the terminology of harmonic constraints has been carried over from X PLOR This feature allows a harmonic restraining force to be applied to any set of atoms in the simulation For further details see the NAMD Programmer s Guide 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
35. aint will be imposed on the distance between the centers of mass of residues 10 to 15 and residues 30 to 35 low 20 0 hi 10 0 indicates that the reference distance is 20 0at A 0 and 10 0at A 1 urestraint dist pmf group insulin 10 to insulin 15 group insulin 30 to insulin 35 kf 20 low 20 0 hi 10 0 1 during the initial 10 ps increase the strength of the forcing restraint to full strength 0 20 kcal mol 2 2 next apply a force to slowly close the distance from 20 to 10 A changes from 0 1 3 accumulate dU dA for another 10 ps stays fixed at 1 4 force the distance back to its initial value of 20 changes from 1 0 pmf task grow time 10 ps print 1 ps j pmf task up time 100 ps j pmf task stop time 10 ps pmf 58 task down time 100 ps 1 force the distance to close from 20 to 10 in 5 steps A changes from 0 gt 1 at each step equilibrate for 10 ps then collect dU dA for another 10 ps ref 18 16 14 12 10 duration 10 10 x 5 100 ps E2 reverse the step above changes from 1 0 0 8 0 6 0 4 0 2 0 0 meti task stepup equiltime 10 ps accumtime 10 ps numsteps 5 print 1 ps meti task stepdown 5 7 7 Appendix Gradient for position restraint E K 5 2 ri rel E K5 2 i Bre Yi tres zi mt V E Ky 2i tref
36. ange nonbonded forces every 2 fs and long range electrostatics every 4 fs e MTSAlgorithm lt MTS algorithm to be used gt Acceptable Values verletI Default Value verletI Description Specifies the multiple timestep algorithm used to integrate the long and short range forces verletI is the same as r RESPA e longSplitting lt how should long and short range forces be split gt Acceptable Values xplor c1 Default Value c1 Description Specifies the method used to split electrostatic forces between long and short range potentials The xplor option uses the X PLOR shifting function and the c1 splitting uses the following C continuous shifting function 6 SW rij 0if Fizl gt Roff SW rij 1 if Iri lt Ron if Roff gt Tijl gt Ron where Ron is a constant defined using the configuration value switchdist Rory is specified using the configuration value cutoff 32 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 e mollyTolerance lt allowable error for MOLL
37. ble Values on or off Default Value off Description Specifies whether or not Langevin piston pressure control is active If set to on then the parameters LangevinPistonTarget LangevinPistonPeriod LangevinPistonDecay and LangevinPistonTemp must be set e LangevinPistonTarget lt target pressure bar gt Acceptable Values positive decimal Description Specifies target pressure for Langevin piston method e LangevinPistonPeriod lt oscillation period fs gt Acceptable Values positive decimal Description Specifies barostat oscillation time scale for Langevin piston method e LangevinPistonDecay lt damping time scale fs gt Acceptable Values positive decimal Description Specifies barostat damping time scale for Langevin piston method 43 e 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 e StrainRate lt initial strain rate gt Acceptable Values decimal triple x y z Default Value 0 0 0 Description Optionally specifies the initial strain rate for pressure control Is overridden by value read from file specified with extendedSystem 5 6 Applied Forces and Analysis Currently there are two ways to steer simulations with NAMD One is called moving constraints and is based on the harmonic const
38. cedure For example loadcoords m and print m 4 e addforce lt atomid groupid gt lt force vector gt Applies force in kcal mol T to atom or group addforce should only be called from within the calcforces procedure For example addforce groupid 1 0 2 P Several vector routines from the VMD Tcl interface are also defined 5 7 Free Energy of Conformational Change Calculations NAMD incorporates methods for performing free energy of conformational change perturbation calculations The system is efficient if only a few coordinates either of individual atoms or centers of mass of groups of atoms are needed The following configuration parameters are used to enable free energy perturbation e freeEnergy lt is free energy perturbation active gt Acceptable Values on or off Default Value off Description Specifies whether or not free energy perturbation is active If it is set to off then no free energy perturbation is performed If it is set to on then the free energy perturbation calculation specified in freeEnergyConfig parameters is executed e freeEnergyConfig lt free energy perturbation script gt Acceptable Values file or script Description Must contain either the name of a free energy perturbation script file or the script itself between and may include multiple lines This parameter may occur multiple times and scripts will be executed in order of appearance The format of the free energy
39. der a pair of atoms A and B that are 8 1 A apart when the pairlist is built If the pair list includes only those atoms within the cutoff distance this pair would not be included in the list Now assume that after five timesteps atoms A and B have moved to only 7 9 A apart A and B are now within the cutoff distance of each other and should have their non bonded interactions calculated However because the non bonded interactions are based solely on the pair list and the pair list will not be rebuilt for another five timesteps this pair will be ignored for five timesteps causing energy not to be conserved within the system To avoid this problem the parameter pairlistdist allowed the user to specify a distance greater than the cutoff distance for pairs to be included in the pair list as shown in Figure 4 Pairs that are included in the pair list but are outside the cutoff distance are simply ignored So in the above example if the pairlistdist were set to 10 0 A then the atom pair A and B would be included in the pair list even though the pair would initially be ignored because they are further apart than the cutoff distance As the pair moved closer and entered the cutoff distance because the pair was already in the pair list the non bonded interactions would immediately be calculated and energy conservation would be preserved The value of pairlistdist should be chosen such that no atom pair moves more than pairlistdist cutoff in one cycle
40. e 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 This option alters this behavior for water molecules only 5 5 Pressure Control 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 This is not currently implemented in Berendsen s method 5 5 1 Berendsen pressure bath coupling NAMD provides constant pressure simulation using Berendsen s method The following parameters are used to define the algorithm 42 e BerendsenPressure lt use Berendsen pressure bath coupling gt Acceptable Values on or off Default Value off Description Specifies whether or not Berendsen pressure bath coupling is active If set to on then the parameters BerendsenPressureTarget B
41. e a Ro9 ee 3 2 NAMD configuration parameters eimi C beh me bo a A ia a a a Aen ee ea aa Wa Output fil s imc tee ee ee RUE huh deos et sU EA ce A Basic Simulation Parameters 4 1 Non bonded interaction parameters and computations 4 1 1 Non bonded van der Waals interactions 4 1 2 Non bonded electrostatic interactions 4 1 3 Nonbonded interaction distance testing 4 2 Fullelectrostaticintegration 4 3 NAMD configuration parameters 4 3 1 Timestepparameters 4 3 2 Simulation space partitioning 433 Basic dynamics 4 34 DPMTA parameters lle 43 0 PME parameters mc yeo a cel DO a A kde UE Oe POR 4 8 6 Full direct parameters 4 8 7 Multiple timestep parameters Additional Simulation Parameters 5 1 Constraints and Restraints 5 1 1 Harmonic constraint parameters 5 1 2 Fixed atoms parameters 5 2 Energy Minimization 5 2 1 Velocity quenching parameters 5 3 Temperature Control and Equilibration 5 3 1 Langevin dynamics parameters 10 12 14 15 15 1
42. e name e TCL definitions for Tcl installation optional e MDCOMM definitions for MDComm installation very optional 4 In the main directory run config lt architecture gt which will create a new build subdi rectory lt architecture gt You only need to repeat this step if you add new source files 5 Change to this new directory and type make 9 4 Documentation All available NAMD documentation is available for download without registration via the NAMD web site http www ks uiuc edu Research namd 70 References 1 2 M P Allen and D J Tildesley Computer Simulation of Liquids Oxford University Press New York 1987 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 J Board Z Hakura W Elliot and W Rankin Scalable variants of multipole accelerated algorithms for molecular dynamics applications Technical Report TR94 006 Duke University Dept of Elec Engr 1994 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 Institu
43. e present e fixedAtomsFile lt PDB file containing fixed atom parameters gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to use for the fixed atom flags for each atom If this parameter is not specified then the PDB file specified by coordinates is used e fixedAtomsCol lt column of PDB containing fixed atom parameters gt Acceptable Values X Y Z 0 or B Default Value 0 Description Column of the PDB file to use for the containing fixed atom parameters for each atom The coefficients can be read from any floating point column of the PDB file A value of O indicates that the atom is not fixed 39 5 2 Energy Minimization 5 2 1 Velocity quenching parameters As described in the NAMD Programmer s Guide NAMD has the capability of performing energy minimization using a simple quenching scheme While this algorithm is not the most rapidly convergent it is sufficient for most applications There are only two parameters for minimization one to activate minimization and another to specify the maximum movement of any atom e minimization lt Perform energy minimization gt Acceptable Values on or off Default Value off Description Turns 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 singl
44. e selectConstraints lt Restrain only selected Cartesian components of the coordinates gt Acceptable Values on or off Default Value off Description This option is useful to restrain the positions of atoms to a plane or a line in space If active this option will ensure that only selected Cartesian components of the coordinates are restrained E g Restraining the positions of atoms to their current z values with no restraints in x and y will allow the atoms to move in the x y plane while retaining their original z coordinate Restraining the x and y values will lead to free motion only along the z coordinate e selectConstrX lt Restrain X components of coordinates gt Acceptable Values on or off Default Value off Description Restrain the Cartesian x components of the positions e selectConstrY lt Restrain Y components of coordinates gt Acceptable Values on or off Default Value off Description Restrain the Cartesian y components of the positions e selectConstrZ lt Restrain Z components of coordinates gt Acceptable Values on or off Default Value off Description Restrain the Cartesian z components of the positions 5 1 2 Fixed atoms parameters Atoms may be held fixed during a simulation NAMD avoids calculating most interactions in which all affected atoms are fixed e fixedAtoms lt are there fixed atoms gt Acceptable Values on or off Default Value off Description Specifies whether or not fixed atoms ar
45. e 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 5 3 Temperature Control and Equilibration 5 3 1 Langevin dynamics parameters As described in the NAMD Programmer s Guide NAMD is capable of performing Langevin dynam ics 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 5 although a different integrator is used e langevin lt use Langevin dynamics gt Acceptable Values on or off Default Value off Description Specifies whether or not Langevin dynamics active If set to on then the parameter langevinTemp must be set and the parameters langevinFile and langevinCol can optionally be set to control the behavior of this feature e langevinTemp lt temperature for Langevin calculations K gt Acceptable 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
46. e workstation clusters for which is was originally designed Future versions of NAMD will also make efficient use of clusters of multi processor workstations or PCs NAMD has several important features e Force Field Compatibility The force field used by NAMD is the same as that used by the programs CHARMM 4 and X PLOR 5 This force field includes local interaction terms consisting of bonded interactions between 2 3 and 4 atoms and pairwise interactions including electrostatic and van der Waals forces This commonality allows simulations to migrate between these three programs e Efficient Full Electrostatics Algorithms NAMD incorporates the Distributed Parallel Multipole Tree Algorithm DPMTA 3 and Distributed Particle Mesh Ewald DPME algorithms which takes the full electrostatic inter actions into account These algorithm reduces the computational complexity of electrostatic force evaluation from O N to O N or 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
47. ential of Mean Force Calculation 5 66 EXampl s cua o EROR RR Pe EU AA Bult Appendiks ce A A O AAA Translation between NAMD and X PLOR configuration parameters Sample configuration files Running NAMD 8 1 Platform Specific Notes ee ee 8 1 1 Network of Workstations 8 1 20 IBM SP3 Kia ouo oko Be A qaum A ds 8 1 3 CRAY TE uo a Rub RR REC EORR RU XU S L cOrngi2000 ies kite wwe gp Aon eee BM apy Gade E mucho tuto 8 2 Interactive modeling with MDScope NAMD Availability and Installation 9 1 How to obtain NA MBI ai a duke GP Abe ues eo oe na Ge Bae 9 2 Platforms on which NAMD willcurrentlyrun 9 3 Compiling NAMD 2 4 02 ee 4 See be xao Ro a RR dU 9 4 Documentation 2 605 fee bck edd SNe YR AO SRR ee ee CERAM EU he A EN 62 64 67 67 67 67 67 68 68 List of Figures 1 Graph of van der Waals potential with and without switching 22 2 Graph of electrostatic potential with and without shifting function 23 3 Graph of electrostatic split between short and long range forces 23 4 Example of cutoff and pairlist distance uses 25 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
48. eractions 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 22 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 fully described in the NAMD Programmer s Guide and is based on the shifting function used by X PLOR energy Sais e 0 t cutoff distance Figure 2 Graph showing an electrostatic potential with and without the application of the shifting function Next consider the case where full electrostatics are calculated In this case the electrostatic interactions are not truncated at any distance In this 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 force
49. erendsenPressureCompressibility and BerendsenPressureRelaxationTime must be set and the parameter BerendsenPressureFreq can optionally be set to control the behavior of this feature e BerendsenPressureTarget lt target pressure bar gt Acceptable Values positive decimal Description Specifies target pressure for Berendsen s method e BerendsenPressureCompressibility lt compressibility bar gt Acceptable Values positive decimal Description Specifies compressibility for Berendsen s method e BerendsenPressureRelaxationTime lt relaxation time fs gt Acceptable Values positive decimal Description Specifies relaxation time for Berendsen s method e BerendsenPressureFreq lt how often to rescale positions gt Acceptable Values positive multiple of nonbondedFrequency and fullElectFrequency Default Value nonbondedFrequency or fullElectFrequency if used Description Specifies number of timesteps between position rescalings for Berendsen s method 5 5 2 Nos Hoover Langevin piston pressure control NAMD provides constant pressure simulation using a modified Nos Hoover method in which Langevin dynamics is used to control fluctuations in the barostat This method should be combined with a method of temperature control such as Langevin dynamics in order to simulate the NPT ensemble The following parameters are used to define the algorithm e LangevinPiston lt use Langevin piston pressure control gt Accepta
50. ergies only occasionally 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 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 outputTiming lt timesteps between timing output gt Acceptable Values nonnegative integer Default Value 0 Description The number of timesteps between each timing output of NAMD If specified and nonzero CPU and wallclock times will be output to stdout These data are from node 0 only CPU times for other nodes may vary 21 4 Basic Simulation Parameters 4 1 Non bonded interaction parameters and computations 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 4 1 1 Non bonded van der Waals interactions The simplest non bonded interaction is the van der Waals interaction In NAMD van der Waals interactions are always truncated at the cutoff distance
51. f the numerical Verlet integrator Improved methods for incorporating these long range forces are currently being investigated with the intention of improving accuracy as well as reducing the frequency of long range force evaluations In the scheme described above the van der Waals forces are still truncated at the local interac tion distance Thus the van der Waals cutoff distance forms a lower limit to the local interaction distance While this is believed to be sufficient there are investigations underway to remove this limitation and provide full van der Waals calculations in O N time as well 25 4 3 NAMD configuration parameters 4 3 1 Timestep parameters e numsteps lt number of timesteps gt Acceptable Values positive integer Description The number of simulation timesteps to be performed An integer greater than 0 is acceptable The total amount of simulation time is numsteps x timestep e timestep lt timestep size fs gt Acceptable Values non negative decimal Default Value 1 0 Description The timestep size to use when integrating each step of the simulation The value is specified in femtoseconds e firsttimestep lt starting timestep value gt Acceptable Values non negative integer Default Value 0 Description The number of the first timestep This value is typically used only when a simulation is a continuation of a previous simulation In this case rather than having the timestep restart at 0 a specific ti
52. ge from 0 to 1 and a value of A 0 corresponds to one defined state and a value of A 1 corresponds to the other defined state Intermediate values of correspond to intermediate states in the case of conformational forcing calculations these intermediate states are physically realizable but in the case of molecular transformation calculations they are not The value of A is changed during the simulation In the first method provided here the change in A is stepwise while in the second method it is virtually continuous Multi configurational thermodynamic integration MCTI In MCTI one accumulates QU OA at several values of A and from these averages estimates the integral AA f 9U 9A dr With this method the precision of each 9U 0A can be estimated from the fluctuations of the time series of JU 0A Slow growth In slow growth A is incremented by A 1 Nstep after each dynamics integration time step and the pmf is estimated as 54 AA X OU OX A Typically slow growth is done in cycles of equilibration at A 0 change to A 1 equilibration at A 1 change to A 0 It is usual to estimate the precision of slow growth simulations from the results of successive cycles 5 7 3 Options for Conformational Restraints User supplied restraint and bounds specifications urestraint n restraint or bound specification see below Restraint Specifications not coupled to pmf calculations posi ATOM
53. ical 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 The structure and design of the program is described in the NAMD Programmer s Guide with sufficient detail to allow additions of such new algorithms 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 11 An initial load balancer assigns patches to processors
54. ified to the host program through a file named nodelist in the user s home directory or can be superseded by the nodelist file in the current directory Details about the syntax of nodelist file can be found in Converse Installation and Usage Manual at http charm cs uiuc edu 8 1 2 IBM SP3 On IBM SP3 you would have to use the scheduler available on the front end of the SP system in order to run NAMD Below we give the description of the commands we use at Argonne National Laboratory s IBM SP3 installation Consult the system documentation or your local system ad ministrator about the details at your site We use the command spsubmit to submit NAMD runs to the SP scheduler at Argonne National Laboratory spsubmit np N maxtime mins namd2 lt config file gt N is the number of processors we request NAMD to run on and mins i the maximum time we expect NAMD to take during this run 8 1 3 CRAY T3E mpprun is the name of the command used to run parallel jobs on CRAY T3E This command can be used as mpprun namd2 lt config file gt pN where N is the number of requested processors However this can be used only when the number of requested processors is less than or equal to 32 For jobs larger than this one has to use queuing facility provided at the site of installation Description of the queuing facilities is out of this document s scope and we leave that up to you to explore 67 8 1 4 Origin2000 Origin2000 version of NAM
55. ignTemp parameter must also be given to specify the target temperature e reassignTemp lt temperature for equilibration K gt Acceptable Values positive decimal Default Value temperature if set otherwise none Description The temperature to which all velocities will be reassigned every reassignFreq timesteps This parameter is valid only if reassignFreq has been set e reassignIncr lt temperature increment for equilibration K gt Acceptable Values decimal Default Value 0 Description In order to allow simulated annealing or other slow heating cooling protocols reassignIncr will be added to reassignTemp after each reassignment Reassignment is carried out at the first timestep The reassignHold parameter may be set to limit the final temperature This parameter is valid only if reassignFreq has been set 38 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 5 4 Boundary Conditions 5 4 1 Spherical harmonic boundary conditions NAMD provides spherical harmonic boundary conditions These boundary conditions can consist of a single potential or a combination of two potentials as described in the NAMD Programmer s Guide The following parameters are used to define these boundary
56. imestep 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 DPMTA calculations gt Acceptable Values positive integer factor of stepspercycle Default Value stepspercycle Description This parameter specifies the number of timesteps between each full elec trostatics evaluation It is recommended that fullElectFrequency be chosen so that the product of fullElectFrequency and timestep does not exceed 4 0 unless rigidBonds all or molly on is specified in which case the upper limit is perhaps doubled e nonbondedFreq lt timesteps between nonbonded evaluation gt Acceptable Values positive integer factor of fullElectFrequency Default Value 1 Description This parameter specifies how often short range nonbonded interactions should be calculated Setting nonbondedFreq between 1 and fullElectFrequency allows triple timestepping where for example one could evaluate bonded forces every 1 fs short r
57. in a list of residues group atomname segname resnum segname resnum group atomname atomname segname resnum segname resnum Examples group ca insulin 10 insulin 12 insulin 14 group 1 ca cb cg insulin 10 insulin 12 insulin 14 group 1 ca cb insulin 10 insulin 12 cg insulin 11 insulin 12 Note Within a group atomname is in effect until a new atomname is used or the keyword all is used atomname will not carry over from group to group This note applies to the paragraph below One or more atomnames in a range of residues group atomname segname resnum to segname resnum group atomname atomname segname resnum to segname resnum Examples group ca insulin 10 to insulin 14 group ca cb cg insulin 10 to insulin 12 group 1 ca cb insulin 10 to insulin 12 all insulin 13 5 7 5 Options for Potential of Mean Force Calculation The pmf and mcti blocks below are used to simultaneously control all forcing restraints specified in urestraint above These blocks are performed consecutively in the order they appear in the config file The pmf block is used to either a smoothly vary A from 0 1 or 1 0 or b set lambda The mcti block is used to vary A from 0 1 or 1 0 in steps so that A is fixed while dU d is accumulated Lamba control for slow growth pmf task up down stop g
58. 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 36 e langevinHydrogen lt Apply Langevin dynamics to hydrogen atoms gt Acceptable Values on or off Default Value on Description If langevinDamping is set then setting langevinHydrogen to off will turn off Langevin dynamics for hydrogen atoms This parameter has no effect if Langevin coupling coefficients are read from a PDB file e langevinFile lt PDB file containing Langevin parameters gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to use for the Langevin coupling coefficients for each atom If this parameter is not specified then the PDB file specified by coordinates is used e 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 5 3 2 Temperature coupling parameters As described in the NAMD Programmer s Guide 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 P
59. inTave have to be specified Then every Tmin timesteps NAMD will compute the average velocity in the current direction over the past Tmin timesteps and compare it to Umin The average velocity is computed simply by min TEO Ti mel 5 Tmin In the case that v min is less than Umin a new direction is chosen and the simulation proceeds Every time the direction is changed the reference point is also changed to T0 new ri t as TinewFmin K gt 6 46 where t is the current timestep and Fmin SMDFmin is the minimum force to which the force imposed by the restraint is reset Thus after the direction is changed to finew the force applied to the atom has an absolute value of Fmin and the direction of finew The time stamp ty is set to current time Choice of new direction The choice of the new random direction is based on the specified initial direction the angle 0e of the cone which has 7 as its axis and the method by which the random numbers are generated The new direction is guaranteed to lie within the specified cone The method can be uniform default or gaussian Uniform method uses uniformly distributed random numbers to find angles y and 0 defining the new direction Angle is a random number between 0 and 360 degrees and 0 is a random number between 0 and 0 2 Gaussian method uses uniformly distributed random numbers to find y and normally distributed random numbers with variance 0 SMDGaussW to
60. 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 Default Value coordinates 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 If no value is given and constraints are active then the same PDB file specified by coordinates will be used instead constraining atoms about their initial positions conskfile lt PDB file containing force constant values gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to use for force constants for harmonic constraints If this parameter is not specified then the PDB file containing initial coordinates specified by coordinates is used conskcol lt column of PDB file containing force constant gt Acceptable Values X Y Z 0 or B Default Value 0 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 34
61. is defined then DCDfreq must also be defined DCDfreq lt timesteps between writing coordinates to trajectory file gt Acceptable Values positive integer Description The number of timesteps between the writing of position coordinates to the trajectory file The initial positions will be included in the trajectory file unless the firsttimestep parameter is set non zero velDCDfile lt velocity trajectory output file gt Acceptable Values UNIX filename Description The binary DCD velocity trajectory filename This file stores the trajectory of all atom velocities using the same format binary DCD as X PLOR If velDCDfile is defined then velDCDfreq must also be defined velDCDfreq lt timesteps between writing velocities to trajectory file gt Acceptable Values positive integer Description The number of timesteps between the writing of velocities to the trajectory file The initial velocities will be included in the trajectory file unless the firsttimestep parameter is set non zero outputEnergies lt timesteps between energy output gt Acceptable Values positive integer Default Value 1 20 Description The number of timesteps between each energy output of NAMD This value specifies how often NAMD should output the current energy values to stdout which can be redirected to a file By default this is done every step For long simulations the amount of output generated by NAMD can be greatly reduced by outputting the en
62. is parameter may be useful for restarts SMDFmin lt value of the force to reset to gt Acceptable Values non negative real Default Value 0 Description The value in pN to which the force gets reset when the direction changes or the average velocity exceeds the given SMDVmax value This parameter is only used if SMDChDir or SMDChForce are on SMDChDir lt Is changing direction option of SMD active gt Acceptable Values on off Default Value off Description If turned on this option allows to change the direction of the reference position movement when the average velocity of the restrained atom in this direction is smaller than the given SMDVmin value Uses settings of SMDVmin SMDVminTave SMDConeAngle SMDChDirMethod SMDVmin lt minimum allowed average velocity of the restrained atom gt Acceptable Values non negative real Description The minimum allowed average velocity in A timestep of the restrained atom in the direction of the reference position movement The averaging time is given by SMDVminTave SMDVminTave lt averaging time for velocity to compare to Vmin gt Acceptable Values positive integer Description The averaging time in timesteps for calculation of the average velocity of the restrained atom and for comparison of this average velocity to SMDVmin SMDConeAngle lt angle of the cone to choose the new direction from gt Acceptable Values non negative Default Value 360 Description The angle
63. ix Description The prefix to use for restart filenames NAMD produces PDB 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 If restartfreq is defined then restartname must also be defined binaryrestart lt use binary restart files gt Acceptable Values yes or no Default Value yes Description Activates the use of binary restart files If this option is set to yes then the restart files will be written in binary rather than PDB format Binary files preserve more accuracy between NAMD restarts than ASCII PDB files but the binary files are not guaran teed to be transportable between computer architectures The utility program flipbinpdb is provided with the Linux Intel version to reformat these files DCDfile lt coordinate trajectory output file gt Acceptable Values UNIX filename Description The binary DCD position coordinate trajectory filename This file stores the trajectory of all atom position coordinates using the same format binary DCD as X PLOR If DCDfile
64. k2 must also be defined e cylindricalBCl2 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 e cylindricalBCk2 lt force constant for second potential gt Acceptable Values non zero decimal Description Force constant for the second harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center e cylindricalBCexp2 lt exponent for second potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for second boundary potential The only likely values to use are 2 and 4 5 4 3 Periodic boundary conditions NAMD provides periodic boundary conditions in 1 2 or 3 dimensions The following parameters are used to define these boundary conditions e cellBasisVectori lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellBasisVector2 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellBasisVector3 lt basis vector for periodic boundaries A gt Acceptable Va
65. l NAMD 2 1 9 1 How to obtain NAMD NAMD may be downloaded from http ww 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 Pre compiled binaries are available for most architectures to which NAMD has been ported 9 2 Platforms on which NAMD will currently run NAMD 2 1 should be portable to any parallel platform with a modern C compiler to which Charm and Converse have been ported Some minor tuning of system parameters or compiler flags may be required NAMD 2 1 has been compiled and tested on the following platforms e Intel PC s Linux e HP PA RISC workstations e Sun UltraSparc workstations ACSI Red IBM SP3 Cray T3D and T3E SGI Origin 2000 Origin 200 and Onyx 2 9 3 Compiling NAMD To compile NAMD for a particular machine follow these steps 1 Obtain the latest release of Charm from http charm cs uiuc edu and compile it for the platforms you wish to use 2 Edit Make charm so that the CHARMBASE variable points to the top directory of your Charm installation 3 The arch directory contains files of the form Makearch lt architecture gt Find the file which is closest to the platform you wish to compile for and edit it You may need to alter some of the following e CXX C compiler e CXXOPTS C compiler options e CC C compiler e COPTS C compiler options 69 e CHARMARCH Charm architectur
66. le would remain unchanged If no value for cwd is specified than all filenames are left unchanged but are assumed to be relative to the directory which contains the configuration file given on the command line Output files e outputname lt output PDB file gt Acceptable Values UNIX filename prefix Description At the end of every simulation NAMD writes two PDB files one containing the final coordinates and another containing the final velocities of all atoms in the simulation This option specifies the file prefix for these two files The position coordinates will be saved to a file named as this prefix with coor appended The velocities will be saved to a file named as this prefix with vel appended For example if the prefix specified using this option was tmp output then the two files would be tmp output coor and tmp output vel e binaryoutput lt use binary output files gt Acceptable Values yes or no Default Value yes Description Activates the use of binary output files If this option is set to yes then the final output files will be written in binary rather than PDB format Binary files preserve more accuracy between NAMD restarts than ASCII PDB files but the binary files are not guaranteed to be transportable between computer architectures The utility program flipbinpdb is provided with the Linux Intel version to reformat these files 19 restartname lt restart files gt Acceptable Values UNIX filename pref
67. least one greater than cutoff is recommended e splitPatch lt how to assign atoms to patches gt Acceptable Values position or hydrogen Default Value hydrogen Description When set to hydrogen hydrogen atoms are kept on the same patch as their parents allowing faster distance checking and rigid bonds e 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 e margin lt extra length in patch dimension A gt Acceptable Values positive decimal Default Value 1 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 For more details about this parameter see the NAMD Programmer s Guide Unless you are very motivated to get the very best possible performance just leave this value at the default 4 3 3 Basic dynamics e exclude lt exclusion policy to use gt Acceptable Values none 1 2 1 3 1 4 or scaled1 4 27 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 excl
68. les are read can be important in cases where duplicate values appear in separate files e paraTypeXplor lt Is the parameter file in X PLOR format gt Acceptable Values on or off Default Value on Description Specifies whether or not the parameter file s are in X PLOR format X PLOR format is the default for parameter files Caveat The PSF file should be also con structed with X PLOR in case of an X PLOR parameter file because X PLOR stores in formation about the multiplicity of dihedrals in the PSF file See the X PLOR manual for details e paraTypeCharmm lt Is the parameter file in CHARMM format gt Acceptable Values on or off Default Value off Description Specifies whether or not the parameter file s are in CHARMM format X PLOR format is the default for parameter files Caveat The information about multiplicity of dihedrals will be obtained directly from the parameter file and the full multiplicity will be used same behavior as in CHARMM If the PSF file originates from X PLOR consecutive multiple entries for the same dihedral indicating the dihedral multiplicity for X PLOR will be ignored e velocities lt velocity PDB file gt Acceptable Values UNIX filename 18 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 binvelocitie
69. 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 Laxmikant Kale Robert Skeel Milind Bhandarkar Robert Brunner Attila Gursoy Neal Krawetz James Phillips Aritomo Shinozaki Krishnan Varadarajan and Klaus Schulten NAMD2 Greater scalability for parallel molecular dynamics J Comp Phys 151 283 312 1999 Electronic documents will include a direct link to the official NAMD page http www ks uiuc edu Research namd One copy of each publication or report will be supplied to Illinois through Dr Gila Budescu at the addresses listed below in Contact Information 7 Should Licensee wish to make comme
70. locity and coordinate files The utility programs flipdcd and flipbinpdb are provided with the Linux Intel version to reformat these files The exact format of these files is very ugly but supported by a wide range of analysis and display programs 3 2 NAMD configuration parameters Input files 17 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 or CHARMM22 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 are allowed for systems that require more than one parameter file For example if three files were needed lines such as parameters parami parameters param2 parameters param3 could be added to the configuration 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 fi
71. lues 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 Al e extendedSystem lt XSC file to read cell parameters from gt Acceptable Values file name Description In addition to coor and vel output files NAMD generates a xsc eXtended System Configuration file which contains the periodic cell parameters and extended system variables such as the strain rate in constant pressure simulations Periodic cell parameters will be read from this file if this option is present ignoring the above parameters e XSTfile lt XST file to write cell trajectory to gt Acceptable Values file name 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 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 Acceptabl
72. m by a spring of stiffness NK so the overall behavior of the system is as if you are pulling with a very stiff spring if N is large In both moving and rotating constraints the force constant that you specify in the constraints pdb file is multiplied by 2 for the force calculation i e if you specified K 0 5 kcal mol in the pdb file the force actually calculated is F 2K R X 1 keal mol A R X SMD feature of namd2 does the calculation without multiplication of the force constant specified in the config file by 2 e rotConstraints lt Are rotating constraints active gt Acceptable Values on or off Default Value off 45 Description Should rotating restraints be applied to the system If set to on then rotConsAxis rotConsPivot and rotConsVel must be defined May not be used with movingConstraints e rotConsAxis lt Axis of rotation gt Acceptable Values vector may be unnormalized Description Axis of rotation Can be any vector It gets normalized before use If the vector is 0 no rotation will be performed but the calculations will still be done e rotConsPivot lt Pivot point of rotation gt Acceptable Values position in A Description Pivot point of rotation The rotation axis vector only gives the direction of the axis Pivot point places the axis in space so that the axis goes through the pivot point e rotConsVel lt Angular velocity of rotation gt Acceptable Values rate in degrees per ti
73. mestep Description Angular velocity of rotation degrees timestep 5 6 3 Steered Molecular Dynamics SMD The SMD feature is independent from the harmonic constraints although it follows the same ideas One has to specify the force constant k SMDk the number 1 based indexing of the atom SMDAtom which is restrained to the moving reference position the initial reference position To SMDRefPos the absolute value of the velocity of movement v SMDVel and the direction of movement 7 SMDDir The velocity Y is then given by Y vri Vector ii is normalized by NAMD before being used Optionally the frequency of SMD data output can be specified The time used in the reference position calculation starts at time to which can be specified through SMDTStamp parameter defaulting to firstTimestep The reference position is calculated then by r To Ru t to 4 where t is the current timestep i e firstTimestep plus however many timesteps have passed since the beginning of NAMD run When restarting the simulation it may be useful to set to to whatever time the reference position specified in the configuration file refers to Changing direction of reference position movement One may want to change the direction of the reference position movement e g if the restrained atom is moving too slow in the given direction To check for such slow movement the minimum allowed average velocity Umin SMDVmin and the averaging time Tmin SMDVm
74. mestep number can be specified e stepspercycle lt timesteps per cycle gt Acceptable Values positive integer Default Value 20 Description Number of timesteps in each cycle Each cycle represents the number of timesteps between pairlist generation and atom reassignment If full electrostatics are active it is also the number of timesteps between full electrostatic evaluation unless fullElectFrequency is also specified It is recommended that stepspercycle fullElectFrequency be chosen so that the product of stepspercycle and timestep does not exceed 4 0 unless rigidBonds all is specified in which case the upper limit is perhaps doubled For more details on the use of full electrostatics see Section 4 2 For more details on non bonded force evaluation and pairlist generation see Section 4 1 4 3 2 Simulation space partitioning e cutoff lt local interaction distance common to both electrostatic and van der Waals calcu lations A gt Acceptable Values positive decimal Description See Section 4 1 for more information e switching lt use switching function gt Acceptable Values on or off Default Value off Description If switching is specified to be off then a truncated cutoff is performed If switching is turned on then smoothing functions are applied to both the electrostatics and van der Waals forces For a complete description of the non bonded force parameters see Section 4 1 If switching is set to on then switchdist
75. mmercial use of the NAMD software or derivative works based thereon REQUIRES A COMMERCIAL LICENSE Commercial use includes 1 integration of all or part of the Software into a product for sale lease or license by or on behalf of Licensee to third parties or 2 distribution of the Software to third parties that need it to commercialize product sold or licensed by or on behalf of Licensee The University of Illinois will negotiate commercial use licenses for NAMD upon request These requests can be directed to namdOks uiuc edu Registration Individuals may register in their own name or with their institutional or corporate affiliations Registration information must include name title and e mail of a person with signature authority to authorize and commit the individuals academic or research institution or corporation as necessary to the terms and conditions of the license agreement The registrant can obtain the NAMD software by completing and submitting the form below Use these guidelines for completion of the questions within the form 1 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 2 Fill in the information sections of the form in detail Your input is very important t
76. must also be defined 26 e switchdist lt distance at which to activate switching function for electrostatic and van der Waals calculations A gt Acceptable Values positive decimal lt cutoff Description Distance at which the switching function should begin to take effect This parameter only has meaning if switching is set to on The value of switchdist must be less than or equal to the value of cutoff since the switching function is only applied on the range from switchdist to cutoff For a complete description of the non bonded force parameters see Section 4 1 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 each cycle containing pairs of atoms for which electrostatics and van der Waals interactions will be calculated This parameter is used when switching is set to on to specify the allowable distance between atoms for inclusion in the pair list This parameter is equivalent to the X PLOR parameter CUTNb If no atom moves more than pairlistdist cutoff during one cycle then there will be no jump in electrostatic or van der Waals energies when the next pair list is built Since such a jump is unavoidable when truncation is used this parameter may only be specified when switching is set to on If this parameter is not specified and switching is set to on the value of cutoff is used A value of at
77. o gain access 1 2 First Name Family Name Title Organization include department or workgroup Estimated number of users at your site Telephone Number Email Address Nature of Use research teaching internal business personal other please explain Contact Information The best contact path for licensing issues is by e mail to namd ks uiuc edu or send correspondence to NAMD Team Theoretical Biophysics Group Beckman Institute University of Illinois 405 North Mathews MC 251 Urbana Illinois 61801 USA FAX 217 244 6078 Contents 1 Introduction 1 1 Newfeaturesinversion2 1 1 2 NAMD and molecular dynamics simulations 1 3 User feedback iia a a Rady bee we a a a Se A BS KA i Acknowledgments is suse mn a eke eee E BOR OE kam de euis Getting Started 2 1 Whatisneeded 4 2s Rak iR RR E a Eo d o9 ERE o RR 2 2 NAM D configuration Ble 2 p gomar p EUSROGORRMRGe s3e amp EaEAGEG iu 2 2 1 Configuration parametersyntak 2 2 2 Required NAMD configuration parameters Input and Output Files Sl EE TOMES e mex A Anche or P RS a Aou Ra bm oe EUG B Xo 3 14 PDB4fles 4 2 ume ESEUER EX ox Rho x RU AE S ee 3 1 2 X PLOR format PSF files 2 o 3 1 3 CHARMMI9 and CHARMM22 parameter files 3 14 DCD trajectory files 0200 kee OW Poe 304
78. o the NAMD development team The NAMD team would like to know the nature of the different projects using NAMD to appraise the probable extent of user communities with certain additional software needs Registration will be administered by the NAMD development team UNIVERSITY OF ILLINOIS NAMD MOLECULAR DYNAMICS SOFTWARE LICENSE AGREEMENT Upon execution of this Agreement by the party identified below Licensee The Board of Trustees of the University of Illinois Illinois on behalf of The Theoretical Biophysics Group TBG in the Beckman Institute will provide the molecular dynamics software NAMD in Executable Code and or Source Code form Software to Licensee subject to the following terms and conditions For purposes of this Agreement Executable Code is the compiled code which is ready to run on Licensee s computer Source code consists of a set of files which contain the actual program commands that are compiled to form the Executable Code 1 The Software is intellectual property owned by Illinois and all right title and interest in cluding copyright remain with Illinois Illinois grants and Licensee hereby accepts a restricted non exclusive non transferable license to use the Software for academic research and internal busi ness purposes only e g not for commercial use see Paragraph 7 below without a fee Licensee agrees to reproduce the copyright notice and other proprietary markings on all copies of
79. oms are left at the final value achieved by ShakeH Although the default value is 100 convergence is usually reached after fewer than 10 iterations 4 3 4 DPMTA parameters These parameters control the options to DPMTA an algorithm used to provide full electrostatic interactions DPMTA is a modified version of the FMA Fast Multipole Algorithm and unfortu nately most of the parameters still refer to FMA rather than DPMTA for historical reasons Don t be confused For a further description of how exactly full electrostatics are incorporated into NAMD see Section 4 2 For a greater level of detail about DPMTA and the specific meaning of its options see the DPMTA distribution which is available via anonymous FTP from the site ftp ee duke edu in the directory pub SciComp src e FMA lt use full electrostatics gt Acceptable Values on or off Default Value off Description Specifies whether or not the DPMTA algorithm from Duke University should be used to compute the full electrostatic interactions If set to on DPMTA will be used with a multiple timestep integration scheme to provide full electrostatic interactions as detailed in Section 4 2 29 e FMALevels lt number of levels to use in multipole expansion gt Acceptable Values positive integer Default Value 5 Description Number of levels to use for the multipole expansion This parameter is only used if FMA is set to on A value of 4 should be sufficient for systems with les
80. on should continue etc Section 2 2 1 describes how options are specified within a NAMD configuration file Section 2 2 2 lists the parameters which are required to run a basic simulation Section 6 describes the relation between specific NAMD and X PLOR dynamics options Several sample NAMD configuration files are shown in section 7 2 2 1 Configuration parameter syntax Each line in the configuration files consists of a keyword identifying the option being specified and a value which is a parameter to be used for this option The keyword and value can be separated by only white space keyword value or the keyword and value can be separated by an equal sign and white space keyword value Blank lines in the configuration file are ignored Comments are prefaced by a and may appear on the end of a line with actual values keyword value This is a comment or may be at the beginning of a line This entire line is a comment 15 Some keywords require several lines of data These are generally implemented to either allow the data to be read from a file keyword filename or to be included inline using Tcl style braces keyword lots of data The specification of the keywords is case insensitive so that any combination of upper and lower case letters will have the same meaning Hence DCDfile and dcdfile are equivalent The capitalization in the values however may be important Some values indicate file names in which capi
81. ovides 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 restrained atom the current force applied to the restrained atom in piconewtons pN the reference position at the time of the last change of direction or force resetting initially the reference position specified in the configuration file current direction of the reference position movement and the time stamp indicating the timestep when the direction was changed or force reset initially SMDTStep specified in the configuration file or its default value The output line starts with word SMD The energy of the SMD restraint is printed out along with other energies in the column titled SMD The frequency of this output is defined by outputEnergies parameter in the configuration file When the direction of the reference position movement changes or the force is reset this change is indicated by an output line starting with SMDChange and showing the current timestep the AT current atom position the new reference position after the change and the new direction of the reference position movement The current timestep becomes the time stamp for the following simulation until the next change occurs Parameters The following parameters describe the parameters for the SMD feature of NAMD This feature allows a harmonic res
82. p insulin 20 insulin 22 group ca insulin 30 to insulin 32 insulin 34 all insulin 35 barr 20 ref 90 Bound specifications 57 1 impose an upper bound if an atom s position strays too far from a reference position add an energy term if the atom is more than 10A from 2 0 2 0 2 0 2 amp 3 impose lower and upper bounds on the distance between the ca s of residues 5 and 15 if the separation is less than 5 0A or greater than 12 0A add an energy term 4 impose a lower bound on the angle between the centers of mass of residues 3 6 9 if the angle goes lower than 90 apply a restraining potential urestraint posi bound insulin 3 cb kf 20 hi 2 0 2 0 2 0 10 0 dist bound insulin 5 ca insulin 15 ca kf 20 low 5 0 dist bound insulin 5 ca insulin 15 ca kf 20 hi 12 0 angle bound insulin 3 insulin 6 insulin 9 kf 20 low 90 0 torsional bounds are defined as pairs this example specifies upper and lower bounds on the dihedral angle X separating the planes of the 1 2 3 residues and the 2 3 4 residues The energy is 0 for 90 ix 1202 The energy is 20 kcal mol for 130 jx 260 Energy rises from 0 20 kcal mol as X increases from 120 130 and decreases from 907 100 urestraint dihe bound insulin 1 insulin 2 insulin 3 insulin 4 gap 20 low 90 hi 120 delta 10 i Forcing restraints a forcing restr
83. ples Fixed restraints 1 restrain the position of the ca atom of residue 0 2 restrain the distance between the ca s of residues 0 and 10 to 5 2 3 restrain the angle between the ca s of residues 0 10 20 to 90 4 restrain the dihedral angle between the ca s of residues 0 10 20 30 to 180 5 restrain the angle between the centers of mass of residues 0 10 20 to 90 urestraint posi insulin 0 ca kf 20 ref 10 11 11 dist insulin 0 ca insulin 10 ca kf 20 ref 5 2 angle insulin 0 ca insulin 10 ca insulin 20 ca kf 20 ref 90 dihe insulin 0 ca insulin 10 ca insulin 20 ca insulin 30 ca barr 20 ref 180 angle insulin 0 insulin 10 insulin 20 kf 20 ref 90 1 restrain the center of mass of three atoms of residue 0 2 restrain the distance between the COM of 3 atoms of residue 0 to the COM of 3 atoms of residue 10 3 restrain the dihedral angle of 10 11 12 15 16 17 18 20 22 30 31 32 34 35 to 90 ca of 10 to 12 ca cb cg of 15 to 18 all atoms of 20 and 22 ca of 30 31 32 34 all atoms of 35 urestraint posi group insulin 0 ca insulin 0 cb insulin 0 cg kf 20 ref 10 11 11 dist group insulin 0 ca insulin 0 cb insulin 0 cg group insulin 10 ca insulin 10 cb insulin 10 cg kf 20 ref 6 2 dihe group ca insulin 10 to insulin 12 group ca cb cg insulin 15 to insulin 18 grou
84. potential with U k x xo and the force with F dk x xo where d is the exponent consexp The result is that if one specifies some value for the force constant k in the PDB file effectively the force constant is 2k in calculations This caveat was removed in SMD feature The following parameters describe the parameters for the moving harmonic constraint feature of NAMD This feature allows the restraint reference positions for all restrained atoms to be moved Moving the restraint reference positions for a single atom is provided by the SMD feature 44 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 5 6 2 Rotating Constraints The constraints parameters are specified in the same manner as for usual static harmonic con straints The reference positions of all constrained atoms are then rotated with a given angular velocity about a given axis If the force constant of the constraints is sufficiently large the con strained atoms will follow their reference positions A rotation matrix M about the axis unit vector
85. raints feature The other is a stand alone feature called SMD In both cases the user specifies a reference position ro force constant k velocity of the reference position movement Y and the number of the constrained atom 1 Then during the simulation a potential Usmp and a corresponding force fou p are added for the specified atom The potential is computed according to Usyup t 1 and the force acting on atom i is by differentiating Usmp fsup t k r t AKON 2 where t is time 7 is the position of the atom 1 and 7 is the current reference position position of the restraint point given by r t To vt 3 5 6 1 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 Eq 3 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 3 where U is in A timestep and t is the current timestep ie 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
86. rcial 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 UNDERSTOOD AND AGREED LICENSEE Licensee must have the authority to authorize and commit the individual academic or research institution or corporation as necessary to the terms and conditions of the license agreement Please fill out the following fields in order t
87. roduce the same results If no value is specified NAMD will choose a pseudo random value based on the current UNIX clock time The random number seed will be output during the simulation startup so that its value is known and can be reused for subsequent simulations Note that if Langevin dynamics are used in a parallel simulation i e a simulation using more than one processor even using the same seed will not guarantee reproducible results e rigidBonds lt controls if and how ShakeH is used gt Acceptable Values none water all Default Value none Description When rigidBonds is all the bond between each hydrogen and its mother atom is fixed to the nominal bond length given in the parameter file When water is selected only the bonds between the hydrogens and the oxygen in water molecules are 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 0 00001 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 at
88. row fade or nogrow time T fs ps or ns default ps lambda Y value of A only needed for stop and nogrow lambdat Z value of A only needed for grow fade and nogrow default 0 print P fs ps or ns or noprint default ps up down stop A is applied to the reference values grow fade nogrow A is applied to Ky A fixed value Ay is used to determine the ref values up grow A changes from 0 1 no value of A is required down fade A changes from 1 0 no value of A is required stop nogrow dU dA is accumulated for single point MCTI 56 Lambda control for automated MCTI meti task stepup stepdown stepgrow or stepfade equiltime T1 fs ps or ns default ps accumtime T2 fs ps or ns default ps numsteps N lambdat Z value of A only needed for stepgrow and stepfade default 0 print P fs ps or ns or noprint default ps stepup stepdown A is applied to the reference values stepgrow stepfade A is applied to Ky A fixed value A is used to determine the ref values stepup stepgrow A changes from 0 1 no value of A is required stepdown stepfade A changes from 1 0 no value of A is required For each task A changes in steps of 1 0 N from 0 1 or 1 0 At each step no data is accumulated for the initial period T1 then dU dA is accumulated for T2 Therefore the total duration of an mcti block is T1 T2 x N 5 7 6 Exam
89. s option must be defined to determine an initial set of velocities Both options cannot be used together e binvelocities lt binary velocity file gt Acceptable Values UNIX filename Description The binary file containing initial velocities for all atoms in the simulation A binary velocity file is created as output from NAMD by activating the binaryrestart or binaryoutput options The binvelocities option should be used as an alternative to velocities Either the temperature or the velocities binvelocities option must be defined to determine an initial set of velocities Both options cannot be used together e bincoordinates lt binary coordinate restart file gt Acceptable Values UNIX filename Description The binary restart file containing initial position coordinate data A binary coordinate restart file is created as output from NAMD by activating the binaryrestart or binaryoutput options Note that in the current implementation at least the bincoordinates option must be used in addition to the coordinates option but the positions specified by coordinates will then be ignored e cwd lt default directory gt Acceptable Values UNIX directory name Description The default directory for input and output files If a value is given all filenames that do not begin with a are assumed to be in this directory For example if cwd is set to scr then a filename of outfile would be modified to scr outfile while a filename of tmp outfi
90. s than 10 000 atoms A value of 5 or greater should be used for larger systems e FMAMp lt number of multipole terms to use for FMA gt Acceptable Values positive integer Default Value 8 Description Number of terms to use in the multipole expansion This parameter is only used if FMA is set to on If the FMAFFT is set to on then this value must be a multiple of 4 The default value of 8 should be suitable for most applications e FMAFFT lt use DPMTA FFT enhancement gt Acceptable Values on or off Default Value on Description Specifies whether or not the DPMTA code should use the FFT enhancement feature This parameter is only used if FMA is set to on If FMAFFT is set to on the value of FMAMp must be set to a multiple of 4 This feature offers substantial benefits only for values of FMAMp of 8 or greater This feature will substantially increase the amount of memory used by DPMTA e FMAtheta DPMTA theta parameter radians gt Acceptable Values decimal Default Value 0 715 Description This parameter specifies the value of the theta parameter used in the DPMTA calculation The default value is based on recommendations by the developers of the code e FMAFFTBlock lt blocking factor for FMA FFT gt Acceptable Values positive integer Default Value 4 Description The blocking factor for the FFT enhancement to DPMTA This parameter is only used if both FMA and FMAFFT are set to on The default value of 4 should be suitable
91. s will be applied using a multiple timestep integration scheme as described in Section 4 2 direct at Et 5 every step a o cutoff 0 t distance Figure 3 Graph showing an electrostatic potential when full electrostatics are used within NAMD with one curve portion calculated directly and the other calculated using DPMTA 23 4 1 3 Nonbonded interaction distance testing The last critical parameter for non bonded interaction calculations is the parameter pairlistdist To reduce the cost of performing the non bonded interactions NAMD 1 X used 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 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 together than the cutoff distance during subsequent timesteps and yet not have their non bonded interactions calculated Let us consider a concrete example to better understand this Assume that the pairlist is built once every ten timesteps and that the cutoff distance is 8 0 A Consi
92. specified in a conformational forcing calculation For example the restraint distance dref depends on A and as A changes two atoms or centers of mass are forced closer together or further apart In this case Ky Kyo the value supplied at input Alternatively the value of Ky may depend upon the coupling parameter A according to Ky Kfo Bounds Position bound 1 atom Force constant Ky reference position Fref and upper or lower reference distance dref Upper bound E Ky 2 d dref for di gt dref else E 0 Lower bound E Ky 2 d dref for di lt dyef else E 0 d ri re Distance bound 2 atoms Force constant Ky and upper or lower reference distance dref Upper bound E Ky 2 dij dref for dij gt dref else E 0 Lower bound E K5 2 dij dref for dij lt dref else E 0 Angle bound 3 atoms Force constant Ky and upper or lower reference angle 0 y Upper bound E Ky 2 0 bref for 0 gt Ores else E 0 Lower bound E Ky 2 0 06 5 for 0 lt Ore else E 0 53 Torsion bound 4 atoms An upper and lower bound must be provided together Energy gap Eo lower AND upper reference angles x1 and x and angle interval Ax X1 x xa E 0 x1 Ax x lt a E G 2 1 cos x x1 x2 x xac Ay E G 2 1 cos x x2 xat Ax lt x a Ax 2m E G G Eo 1 cos Ax Bounds may be used in pairs to set a
93. stance 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 39 Description Force constant for the second harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center sphericalBCexp2 lt exponent for second potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for second boundary potential The only likely values to use are 2 and 4 5 4 2 Cylindrical harmonic boundary conditions NAMD provides cylindrical harmonic boundary conditions These boundary conditions can consist of a single potential or a combination of two potentials as described in the NAMD Programmer s Guide The following parameters are used to define these boundary conditions cylindricalBC lt use cylindrical boundary conditions gt Acceptable Values on or off Default Value off Description Specifies whether or not cylindrical boundary conditions are to be applied to the system If set to on then cylindricalBCCenter cylindricalBCr1 cylindricalBCl1 and cylindricalBCk1 must be defined and cylindricalBCAxis cylindricalBCexp1 cylindricalBCr2 cylindricalBC12 cylindricalBCk2 and cylindricalBCexp2 can optionally be defined cylindricalBCCenter lt center of cylinder A gt Acceptable Values position
94. such that the computational load is balanced as much as possible During the simulation an incremental load balancer monitors the load and performs necessary adjustments 1 3 User feedback If you have problems installing or running NAMD after reading this document please send a complete description of the problem by email to namd ks uiuc edu If you discover and fix a problem not described in this manual or the NAMD Programmer s Guide we would appreciate if you would tell us about this as well so we can alert other users and incorporate the fix into the public distribution We are interested in making NAMD more useful to the molecular modeling community Please take a few minutes to complete the short survey on the next page and mail or fax it to NAMD Support Theoretical Biophysics Group Beckman Institute University of Illinois 405 N Mathews St Urbana IL 61801 FAX 217 244 6078 or email the relevant information to namd ks uiuc edu with subject Survey This will help us make NAMD relevant and responsive to the needs of our user community 12 10 11 Name Company University Address Email address Research area Molecular systems to be studied with NAMD NAMD features most useful for your research Irun NAMD on the following platforms and operating systems I would like to run NAMD on How can we improve the NAMD documentation Other comments 13 1 4 Acknowledgments
95. talization is critical Other values such as on or off are case insensitive 2 2 2 Required NAMD configuration parameters The following parameters are required for every NAMD simulation e numsteps page 26 e coordinates page 18 e structure page 18 e parameters page 18 e exclude page 28 e outputname page 19 e one of the following three temperature page 28 velocities page 19 binvelocities page 19 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 16 3 Input and Output Files NAMD was developed to be compatible with existing molecular dynamics packages especially the packages X PLOR 5 and CHARMM 4 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
96. te and Department of Molecular Biophysics and Biochemistry Yale University 1992 W Humphrey and A Dalke VMD user guide Version 0 94 Beckman Institute Technical Report TB 94 07 University of Illinois 1994 J A McCammon and S C Harvey Dynamics of Proteins and Nucleic Acids Cambridge University Press Cambridge 1987 71
97. the Soft ware Licensee has no right to transfer or sublicense the Software to any unauthorized person or entity However Licensee does have the right to make complimentary works that interoperate with NAMD to freely distribute such complimentary works and to direct others to the TBG server to obtain copies of NAMD itself 2 Licensee may at its own expense modify the Software to make derivative works for its own academic research and internal business purposes Licensee s distribution of any derivative work is also subject to the same restrictions on distribution and use limitations that are specified herein for Illinois Software Prior to any such distribution the Licensee shall require the recipient of the Licensee s derivative work to first execute a license for NAMD with Illinois in accordance with the terms and conditions of this Agreement Any derivative work should be clearly marked and renamed to notify users that it is a modified version and not the original NAMD code distributed by Illinois 3 Except as expressly set forth in this Agreement THIS SOFTWARE IS PROVIDED AS IS AND ILLINOIS MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND EITHER EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO WARRANTIES OR MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY PATENT TRADE MARK OR OTHER RIGHTS LICENSEE ASSUMES THE ENTIRE RISK AS TO THE RE SULTS AND PERFORMANCE
98. to use in SMD simulation gt Acceptable Values positive real Description SMD harmonic constraint force constant Must be specified in kcal mol A The conversion factor is 1 kcal mol 69 479 pN A e SMDVel lt Velocity of the SMD reference position movement gt Acceptable Values positive real A timestep Description The velocity of the SMD reference position movement Gives the absolute value e SMDDir lt Direction of the SMD reference position 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 NAMDbefore being used e SMDAtom lt Index 1 based of the atom constrained to the moving reference position gt Acceptable Values positive integer 48 Description The index of the atom constrained to the moving reference position If the atom is numbered N in the PDB file N must be specified SMDOutputFreg lt frequency of SMD output gt Acceptable Values positive integer Default Value 1 Description The frequency in timesteps with which the current SMD data values are printed out SMDTStamp lt time of the last change in reference position gt Acceptable Values non negative integer Default Value firstTimestep Description The timestep at which the reference position rj was last reset Normally it would be the firstTimestep but if the force or direction was reset during the simulation th
99. training force to be applied to any ONE atom in the simulation and the restraining reference position to be moved It also allows to randomly change the direction of the reference position movement if the restrained atom progress is too slow and to reset the applied force to a given value if the progress of the restrained atom is too fast 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 SMDRefPos SMDVel SMDDir and SMDAtom must be defined Also SMDOutputFreq SMDChDir and associated parameters SMDChForce and associated parameters and SMDTStamp can be optionally defined e SMDexp lt exponent to use in SMD harmonic constraint energy function gt Acceptable Values positive even integer Default Value 2 Description Exponent to be used in the SMD harmonic constraint energy function This value must be a positive integer and only even values really make sense This parameter is only used if SMD is set to on e SMDRefPos lt SMD constraint reference position gt Acceptable Values vector Description Vector to use for the initial reference position for the SMD harmonic con straints The atom that is specified by SMDAtom will be initially constrained to this reference position During the simulation this reference position will move with velocity SMDVel in the direction SMDDir e SMDk lt force constant
100. uded With the value of 1 2 all atom pairs that are directly connected via a linear bond will be excluded With the value of 1 3 all 1 2 pairs will be excluded along with all pairs of atoms that are bonded to a common third atom i e if atom A is bonded to atom B and atom B is bonded to atom C then the atom pair A C would be excluded With the value of 1 4 all 1 3 pairs will be excluded along with all pairs connected by a set of two bonds i e if atom A is bonded to atom B and atom B is bonded to atom C and atom C is bonded to atom D then the atom pair A D would be excluded With the value of scaledi 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 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 COMmotion lt allow center of mass motion gt Acceptable Values yes or no Default Value
101. ven SMDVmax value Uses settings of SMDVmax and SMDVmaxTave e SMDVmax lt maximum allowed average velocity of the restrained atom gt Acceptable Values non negative real Description The maximum allowed average velocity in A timestep of the restrained atom in the direction of the reference position movement The averaging time is given by SMDVmaxTave e SMDVmaxTave lt averaging time for velocity to compare to Vmax gt Acceptable Values positive integer Description The averaging time in timesteps for calculation of the average velocity of the restrained atom and for comparison of this average velocity to SMDVmax 5 6 4 Interactive Molecular Dynamics IMD NAMD now works directly with VMD to allow you to view and interactively steer your simulation NAMD will wait for VMD to connect on startup e IMDon lt is IMD active gt Acceptable Values on or off Default Value off Description Specifies whether or not to expect and wait for a 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 NAMD will wait for a connection on this port This number will have to be entered into VMD e IMDfreq lt timesteps between sending coordinates gt Acceptable Values positive integer 50 Description This allows coordinates to be sent less often which may increase NAMD performance or be necessary due to a
102. ycle temperature switching switchdist cutoff pairlistdist 0 5 10000 scratch alanin psf alanin params alanin pdb scaledi 4 0 4 output 1 0 10 300 0 O ON ooo DPMTA parameters FMA FMAMp FMALevels FMAFFT FMAFFTBlock on 8 3 on 4 Specify a working directory 66 8 Running NAMD NAMD currently runs on network of HP Sun SGI and Linux workstations as well as Cray T3E IBM SP3 and SGI CRAY Origin 2000 machines On network of workstations a host program called conv host is needed to launch NAMD on individual workstations in the network This host program is included with the distribution The general command line syntax for invoking NAMD on each of these platforms is lt hostprog gt namd2 lt config file gt pN Where lt config file gt is the name of the configuration file And Nis the number of processors to be used for execution 8 1 Platform Specific Notes The following subsections explain in detail the steps involved in running NAMD on particular platforms 8 1 1 Network of Workstations In order to run NAMD on network of workstations a host program called conv host is needed in order to launch NAMD on individual workstations This program is bundled with the binary distri bution T he names of individual workstations as well as other control information such as how many processes to create on those workstations should they happen to be multiprocessor workstations is spec

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