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Contents
- 1-4scaling parameter
- Non-bonded force field parameters
- centers parameter
- Harmonic restraints and Steered
- targetCenters parameter
- Harmonic restraints and Steered
- targetForceConstant parameter
- Harmonic restraints and Steered
- targetForceExponent parameter
- Harmonic restraints and Steered
- targetNumSteps parameter
- Harmonic restraints and Steered
- targetNumStages parameter
- Harmonic restraints and Steered
- colvars parameter
- NAMD parameters
- colvarsConfig parameter
- NAMD parameters
- colvarsInput parameter
- NAMD parameters
- colvarsTrajFrequency parameter
- Colvars module configuration file
- colvarsTrajAppend parameter
- Colvars module configuration file
- colvarsRestartFrequency parameter
- Colvars module configuration file
- analysis parameter
- Colvars module configuration file
- name parameter
- Declaring and using collective
- width parameter
- Declaring and using collective
- lowerBoundary parameter
- Declaring and using collective
- upperBoundary parameter
- Declaring and using collective
- expandBoundaries parameter
- Declaring and using collective
- lowerWall parameter
- Declaring and using collective
- lowerWallConstant parameter
- Declaring and using collective
- upperWall parameter
- Declaring and using collective
- upperWallConstant parameter
- Declaring and using collective
- outputValue parameter
- Declaring and using collective
- outputVelocity parameter
- Declaring and using collective
- outputSystemForce parameter
- Declaring and using collective
- outputAppliedForce parameter
- Declaring and using collective
- extendedLagrangian parameter
- Declaring and using collective
- extendedFluctuation parameter
- Declaring and using collective
- extendedTimeConstant parameter
- Declaring and using collective
- period parameter
- Periodic components.
- wrapAround parameter
- Periodic components.
- group1 parameter
- Component distance: center-of-mass distance
- group2 parameter
- Component distance: center-of-mass distance
- forceNoPBC parameter
- Component distance: center-of-mass distance
- oneSiteSystemForce parameter
- Component distance: center-of-mass distance
- main parameter
- Component distanceZ: projection of
- ref parameter
- Component distanceZ: projection of
- ref2 parameter
- Component distanceZ: projection of
- axis parameter
- Component distanceZ: projection of
- forceNoPBC parameter
- Component distanceZ: projection of
- oneSiteSystemForce parameter
- Component distanceZ: projection of
- oneSiteSystemForce parameter
- Component dihedral: torsional angle
- cutoff parameter
- Component coordNum: coordination number
- expNumer parameter
- Component coordNum: coordination number
- expDenom parameter
- Component coordNum: coordination number
- cutoff3 parameter
- Component coordNum: coordination number
- group2CenterOnly parameter
- Component coordNum: coordination number
- atoms parameter
- Component rmsd: root mean
- refPositions parameter
- Component rmsd: root mean
- refPositionsFile parameter
- Component rmsd: root mean
- refPositionsCol parameter
- Component rmsd: root mean
- refPositionsColValue parameter
- Component rmsd: root mean
- vector parameter
- Component eigenvector: projection of
- vectorFile parameter
- Component eigenvector: projection of
- vectorCol parameter
- Component eigenvector: projection of
- vectorColValue parameter
- Component eigenvector: projection of
- closestToQuaternion parameter
- Component orientation: orientation from
- residueRange parameter
- Component alpha:
-helix content
- psfSegID parameter
- Component alpha: -helix content
- hBondCoeff parameter
- Component alpha: -helix content
- angleRef parameter
- Component alpha: -helix content
- angleTol parameter
- Component alpha: -helix content
- hBondCutoff parameter
- Component alpha: -helix content
- hBondExpNumer parameter
- Component alpha: -helix content
- hBondExpDenom parameter
- Component alpha: -helix content
- componentCoeff parameter
- Linear and polynomial combinations
- componentExp parameter
- Linear and polynomial combinations
- atomNumbers parameter
- Defining atom groups
- atomNumbersRange parameter
- Defining atom groups
- atomNameResidueRange parameter
- Defining atom groups
- psfSegID parameter
- Defining atom groups
- atomsFile parameter
- Defining atom groups
- atomsCol parameter
- Defining atom groups
- atomsColValue parameter
- Defining atom groups
- dummyAtom parameter
- Defining atom groups
- centerReference parameter
- Defining atom groups
- rotateReference parameter
- Defining atom groups
- refPositions parameter
- Defining atom groups
- refPositionsFile parameter
- Defining atom groups
- refPositionsCol parameter
- Defining atom groups
- refPositionsColValue parameter
- Defining atom groups
- refPositionsGroup parameter
- Defining atom groups
- disableForces parameter
- Defining atom groups
- corrFunc parameter
- Statistical analysis of individual
- corrFuncWithColvar parameter
- Statistical analysis of individual
- corrFuncType parameter
- Statistical analysis of individual
- corrFuncNormalize parameter
- Statistical analysis of individual
- corrFuncLength parameter
- Statistical analysis of individual
- corrFuncStride parameter
- Statistical analysis of individual
- corrFuncOffset parameter
- Statistical analysis of individual
- corrFuncOutputFile parameter
- Statistical analysis of individual
- runAve parameter
- Statistical analysis of individual
- runAveLength parameter
- Statistical analysis of individual
- runAveStride parameter
- Statistical analysis of individual
- runAveOutputFile parameter
- Statistical analysis of individual
- name parameter
- Biasing and analysis methods
- colvars parameter
- Biasing and analysis methods
- name parameter
- Metadynamics calculations
- hillWeight parameter
- Metadynamics calculations
- newHillFrequency parameter
- Metadynamics calculations
- hillWidth parameter
- Metadynamics calculations
- useGrids parameter
- Metadynamics calculations
- gridsUpdateFrequency parameter
- Metadynamics calculations
- dumpFreeEnergyFile parameter
- Metadynamics calculations
- saveFreeEnergyFile parameter
- Metadynamics calculations
- rebinGrids parameter
- Metadynamics calculations
- keepHills parameter
- Metadynamics calculations
- multipleReplicas parameter
- Metadynamics calculations
- replicaID parameter
- Metadynamics calculations
- replicaFilesRegistry parameter
- Metadynamics calculations
- replicaUpdateFrequency parameter
- Metadynamics calculations
- writeHillsTrajectory parameter
- Metadynamics calculations
- forceConstant parameter
- Harmonic restraints and Steered
- alchCol parameter
- Implementation of the free
- alchDecouple parameter
- Implementation of the free
- alchElecLambdaStart parameter
- Implementation of the free
- alchEquilSteps parameter
- Implementation of the free
- alchFile parameter
- Implementation of the free
- alchLambda parameter
- Implementation of the free
- alchLambda2 parameter
- Implementation of the free
- alchOn parameter
- Implementation of the free
- alchOutFile parameter
- Implementation of the free
- alchOutFreq parameter
- Implementation of the free
- alchType parameter
- Implementation of the free
- alchVdwLambdaEnd parameter
- Implementation of the free
- alchVdwShiftCoeff parameter
- Implementation of the free
- alias psfgen command
- List of Commands
| List of Commands
- amber parameter
- AMBER force field parameters
- ambercoor parameter
- AMBER force field parameters
- applyBias parameter
- Parameters for ABF
- Atoms moving too fast
- Non-bonded interaction distance-testing
- auto psfgen command
- List of Commands
- Bad global exclusion count
- Non-bonded interaction distance-testing
- BerendsenPressure parameter
- Berendsen pressure bath coupling
- BerendsenPressureCompressibility parameter
- Berendsen pressure bath coupling
- BerendsenPressureFreq parameter
- Berendsen pressure bath coupling
- BerendsenPressureRelaxationTime parameter
- Berendsen pressure bath coupling
- BerendsenPressureTarget parameter
- Berendsen pressure bath coupling
- binaryoutput parameter
- Output files
- binaryrestart parameter
- Output files
- bincoordinates parameter
- Input files
- binvelocities parameter
- Input files
- BOUNDARY energy
- Standard output
- callback command
- Tcl scripting interface and
- cellBasisVector1 parameter
- Periodic boundary conditions
- cellBasisVector2 parameter
- Periodic boundary conditions
- cellBasisVector3 parameter
- Periodic boundary conditions
- cellOrigin parameter
- Periodic boundary conditions
- checkpoint command
- Tcl scripting interface and
- COMmotion parameter
- Initialization
- consexp parameter
- Harmonic restraint parameters
- consForceFile parameter
- Constant Forces
- consForceScaling parameter
- Constant Forces
- conskcol parameter
- Harmonic restraint parameters
- conskfile parameter
- Harmonic restraint parameters
- consref parameter
- Harmonic restraint parameters
- constantForce parameter
- Constant Forces
- constraints parameter
- Harmonic restraint parameters
- constraintScaling parameter
- Harmonic restraint parameters
- coord psfgen command
- List of Commands
- coordinates parameter
- Input files
- coordpdb psfgen command
- List of Commands
- coorfile command
- Tcl scripting interface and
- cutoff parameter
- Non-bonded force field parameters
- cwd parameter
- Input files
- cylindricalBC parameter
- Cylindrical harmonic boundary conditions
- cylindricalBCAxis parameter
- Cylindrical harmonic boundary conditions
- cylindricalBCCenter parameter
- Cylindrical harmonic boundary conditions
- cylindricalBCexp1 parameter
- Cylindrical harmonic boundary conditions
- cylindricalBCexp2 parameter
- Cylindrical harmonic boundary conditions
- cylindricalBCk1 parameter
- Cylindrical harmonic boundary conditions
- cylindricalBCk2 parameter
- Cylindrical harmonic boundary conditions
- cylindricalBCl1 parameter
- Cylindrical harmonic boundary conditions
- cylindricalBCl2 parameter
- Cylindrical harmonic boundary conditions
- cylindricalBCr1 parameter
- Cylindrical harmonic boundary conditions
- cylindricalBCr2 parameter
- Cylindrical harmonic boundary conditions
- DCDfile parameter
- Output files
- DCDfreq parameter
- Output files
- DCDUnitCell parameter
- Output files
- delatom psfgen command
- List of Commands
- dielectric parameter
- Non-bonded force field parameters
- eField parameter
- External Electric Field
- eFieldOn parameter
- External Electric Field
- error message
- Atoms moving too fast
- Non-bonded interaction distance-testing
- Bad global exclusion count
- Non-bonded interaction distance-testing
- exclude parameter
- Non-bonded force field parameters
- ExcludeFromPressure parameter
- Nosé-Hoover Langevin piston pressure
- ExcludeFromPressureCol parameter
- Nosé-Hoover Langevin piston pressure
- ExcludeFromPressureFile parameter
- Nosé-Hoover Langevin piston pressure
- extCoordFilename parameter
- External Program Forces
- extendedSystem parameter
- Periodic boundary conditions
- extForceFilename parameter
- External Program Forces
- extForces parameter
- External Program Forces
- extForcesCommand parameter
- External Program Forces
- extraBonds parameter
- Extra bond, angle, and
- extraBondsFile parameter
- Extra bond, angle, and
- FFTWEstimate parameter
- PME parameters
- FFTWUseWisdom parameter
- PME parameters
- FFTWWisdomFile parameter
- PME parameters
- first psfgen command
- List of Commands
- firsttimestep parameter
- Timestep parameters
- fixedAtoms parameter
- Fixed atoms parameters
- fixedAtomsCol parameter
- Fixed atoms parameters
- fixedAtomsFile parameter
- Fixed atoms parameters
- fixedAtomsForces parameter
- Fixed atoms parameters
- FullDirect parameter
- Full direct parameters
- fullElectFrequency parameter
- Multiple timestep parameters
- fullSamples parameter
- Parameters for ABF
- GPRESSAVG
- Standard output
- GPRESSURE
- Standard output
- grocoorfile parameter
- GROMACS force field parameters
- gromacs parameter
- GROMACS force field parameters
- grotopfile parameter
- GROMACS force field parameters
- guesscoord psfgen command
- List of Commands
- hgroupCutoff (Å) parameter
- Non-bonded interaction distance-testing
- hideJacobian parameter
- Parameters for ABF
- IMDfreq parameter
- Interactive Molecular Dynamics (IMD)
- IMDignore parameter
- Interactive Molecular Dynamics (IMD)
- IMDon parameter
- Interactive Molecular Dynamics (IMD)
- IMDport parameter
- Interactive Molecular Dynamics (IMD)
- IMDwait parameter
- Interactive Molecular Dynamics (IMD)
- inputPrefix parameter
- Parameters for ABF
- langevin parameter
- Langevin dynamics parameters
- langevinCol parameter
- Langevin dynamics parameters
- langevinDamping parameter
- Langevin dynamics parameters
- langevinFile parameter
- Langevin dynamics parameters
- langevinHydrogen parameter
- Langevin dynamics parameters
- LangevinPiston parameter
- Nosé-Hoover Langevin piston pressure
- LangevinPistonDecay parameter
- Nosé-Hoover Langevin piston pressure
- LangevinPistonPeriod parameter
- Nosé-Hoover Langevin piston pressure
- LangevinPistonTarget parameter
- Nosé-Hoover Langevin piston pressure
- LangevinPistonTemp parameter
- Nosé-Hoover Langevin piston pressure
- langevinTemp parameter
- Langevin dynamics parameters
- last psfgen command
- List of Commands
- les parameter
- Simulation
- lesCol parameter
- Simulation
- lesFactor parameter
- Simulation
- lesFile parameter
- Simulation
- lesReduceMass parameter
- Simulation
- lesReduceTemp parameter
- Simulation
- limitdist parameter
- Non-bonded force field parameters
- LJcorrection parameter
- Non-bonded force field parameters
- longSplitting parameter
- Multiple timestep parameters
- loweAndersen parameter
- Lowe-Andersen dynamics parameters
- loweAndersenCutoff parameter
- Lowe-Andersen dynamics parameters
- loweAndersenRate parameter
- Lowe-Andersen dynamics parameters
- loweAndersenTemp parameter
- Lowe-Andersen dynamics parameters
- margin parameter
- Non-bonded interaction distance-testing
- margin violations
- Non-bonded interaction distance-testing
- maximumMove parameter
- Velocity quenching parameters
- measure command
- Tcl scripting interface and
- mergeCrossterms parameter
- Standard output
- mgridforce parameter
- Grid Forces
- mgridforcechargecol parameter
- Grid Forces
- mgridforcecol parameter
- Grid Forces
- mgridforcecont1 parameter
- Grid Forces
- mgridforcecont2 parameter
- Grid Forces
- mgridforcecont3 parameter
- Grid Forces
- mgridforcefile parameter
- Grid Forces
- mgridforcepotfile parameter
- Grid Forces
- mgridforcescale parameter
- Grid Forces
- mgridforcevoff parameter
- Grid Forces
- mgridforcevolts parameter
- Grid Forces
- minBabyStep parameter
- Conjugate gradient parameters
- minimization parameter
- Conjugate gradient parameters
- minimize command
- Tcl scripting interface and
- minLineGoal parameter
- Conjugate gradient parameters
- minTinyStep parameter
- Conjugate gradient parameters
- MISC energy
- Standard output
- molly parameter
- Multiple timestep parameters
- mollyIterations parameter
- Multiple timestep parameters
- mollyTolerance parameter
- Multiple timestep parameters
- movingConstraints parameter
- Moving Constraints
- movingConsVel parameter
- Moving Constraints
- MTSAlgorithm parameter
- Multiple timestep parameters
- multiply psfgen command
- List of Commands
- mutate psfgen command
- List of Commands
- nonbondedFreq parameter
- Multiple timestep parameters
- nonbondedScaling parameter
- Non-bonded force field parameters
- numsteps parameter
- Timestep parameters
- OPLS
- Non-bonded force field parameters
- output command
- Tcl scripting interface and
- outputEnergies parameter
- Standard output
- outputFreq parameter
- Parameters for ABF
| Multidimensional histograms
- outputMomenta parameter
- Standard output
- outputname parameter
- Output files
- outputPairlists parameter
- Non-bonded interaction distance-testing
- outputPressure parameter
- Standard output
- outputTiming parameter
- Standard output
- pairInteraction parameter
- Pair interaction calculations
- pairInteractionCol parameter
- Pair interaction calculations
- pairInteractionFile parameter
- Pair interaction calculations
- pairInteractionGroup1 parameter
- Pair interaction calculations
- pairInteractionGroup2 parameter
- Pair interaction calculations
- pairInteractionSelf parameter
- Pair interaction calculations
- pairlistdist parameter
- Non-bonded interaction distance-testing
- pairlistGrow parameter
- Non-bonded interaction distance-testing
- pairlistMinProcs parameter
- Non-bonded interaction distance-testing
- pairlistShrink parameter
- Non-bonded interaction distance-testing
- pairlistsPerCycle parameter
- Non-bonded interaction distance-testing
- pairlistTrigger parameter
- Non-bonded interaction distance-testing
- parameters parameter
- Input files
- paraTypeCharmm parameter
- Input files
- paraTypeXplor parameter
- Input files
- parmfile parameter
- AMBER force field parameters
- patch psfgen command
- List of Commands
- pdb psfgen command
- List of Commands
- pdbalias atom psfgen command
- List of Commands
- pdbalias residue psfgen command
- List of Commands
- PME parameter
- PME parameters
- PMEGridSizeX parameter
- PME parameters
- PMEGridSizeY parameter
- PME parameters
- PMEGridSizeZ parameter
- PME parameters
- PMEGridSpacing parameter
- PME parameters
- PMEInterpOrder parameter
- PME parameters
- PMEProcessors parameter
- PME parameters
- PMETolerance parameter
- PME parameters
- PRESSAVG
- Standard output
- pressureProfile parameter
- Pressure profile calculations
- pressureProfileAtomTypes parameter
- Pressure profile calculations
- pressureProfileAtomTypesCol parameter
- Pressure profile calculations
- pressureProfileAtomTypesFile parameter
- Pressure profile calculations
- pressureProfileEwald parameter
- Pressure profile calculations
- pressureProfileEwaldX parameter
- Pressure profile calculations
- pressureProfileEwaldY parameter
- Pressure profile calculations
- pressureProfileEwaldZ parameter
- Pressure profile calculations
- pressureProfileFreq parameter
- Pressure profile calculations
- pressureProfileSlabs parameter
- Pressure profile calculations
- print command
- Tcl scripting interface and
- psfcontext create psfgen command
- List of Commands
- psfcontext delete psfgen command
- List of Commands
- psfcontext eval psfgen command
- List of Commands
- psfcontext psfgen command
- List of Commands
- psfcontext reset psfgen command
- List of Commands
- psfcontext stats psfgen command
- List of Commands
- ramd accel parameter
- Random acceleration molecular dynamics
- ramd debugLevel parameter
- Random acceleration molecular dynamics
- ramd firstProtAtom parameter
- Random acceleration molecular dynamics
- ramd firstRamdAtom parameter
- Random acceleration molecular dynamics
- ramd forceOutFreq parameter
- Random acceleration molecular dynamics
- ramd lastProtAtom parameter
- Random acceleration molecular dynamics
- ramd lastRamdAtom parameter
- Random acceleration molecular dynamics
- ramd maxDist parameter
- Random acceleration molecular dynamics
- ramd mdStart parameter
- Random acceleration molecular dynamics
- ramd mdSteps parameter
- Random acceleration molecular dynamics
- ramd ramdSeed parameter
- Random acceleration molecular dynamics
- ramd ramdSteps parameter
- Random acceleration molecular dynamics
- ramd rMinMd parameter
- Random acceleration molecular dynamics
- ramd rMinRamd parameter
- Random acceleration molecular dynamics
- readexclusions parameter
- AMBER force field parameters
- readpsf psfgen command
- List of Commands
- reassignFreq parameter
- Temperature reassignment parameters
- reassignHold parameter
- Temperature reassignment parameters
- reassignIncr parameter
- Temperature reassignment parameters
- reassignTemp parameter
- Temperature reassignment parameters
- regenerate psfgen command
- List of Commands
- reinitvels command
- Tcl scripting interface and
- reloadCharges command
- Tcl scripting interface and
- replica exchange
- Replica exchange simulations
- rescaleFreq parameter
- Temperature rescaling parameters
- rescaleTemp parameter
- Temperature rescaling parameters
- rescalevels command
- Tcl scripting interface and
- resetpsf psfgen command
- List of Commands
- residue psfgen command
- List of Commands
- restartfreq parameter
- Output files
- restartname parameter
- Output files
- restartsave parameter
- Output files
- rigidBonds parameter
- Bond constraint parameters
- rigidDieOnError parameter
- Bond constraint parameters
- rigidIterations parameter
- Bond constraint parameters
- rigidTolerance parameter
- Bond constraint parameters
- rotConsAxis parameter
- Rotating Constraints
- rotConsPivot parameter
- Rotating Constraints
- rotConstraints parameter
- Rotating Constraints
- rotConsVel parameter
- Rotating Constraints
- run command
- Tcl scripting interface and
- scnb parameter
- AMBER force field parameters
- seed parameter
- Initialization
- segment psfgen command
- List of Commands
- selectConstraints parameter
- Harmonic restraint parameters
- selectConstrX parameter
- Harmonic restraint parameters
- selectConstrY parameter
- Harmonic restraint parameters
- selectConstrZ parameter
- Harmonic restraint parameters
- SMD parameter
- Parameters
- SMDDir parameter
- Parameters
- SMDFile parameter
- Parameters
- SMDk parameter
- Parameters
- SMDOutputFreq parameter
- Parameters
- SMDVel parameter
- Parameters
- source command
- Tcl scripting interface and
- sphericalBC parameter
- Spherical harmonic boundary conditions
- sphericalBCCenter parameter
- Spherical harmonic boundary conditions
- sphericalBCexp1 parameter
- Spherical harmonic boundary conditions
- sphericalBCexp2 parameter
- Spherical harmonic boundary conditions
- sphericalBCk1 parameter
- Spherical harmonic boundary conditions
- sphericalBCk2 parameter
- Spherical harmonic boundary conditions
- sphericalBCr1 parameter
- Spherical harmonic boundary conditions
- sphericalBCr2 parameter
- Spherical harmonic boundary conditions
- splitPatch parameter
- Non-bonded interaction distance-testing
- stepspercycle parameter
- Non-bonded interaction distance-testing
- StrainRate parameter
- Nosé-Hoover Langevin piston pressure
- structure parameter
- Input files
- SurfaceTensionTarget parameter
- Nosé-Hoover Langevin piston pressure
- switchdist parameter
- Non-bonded force field parameters
- switching parameter
- Non-bonded force field parameters
- tclBC parameter
- Tcl Boundary Forces
- tclBCArgs parameter
- Tcl Boundary Forces
- tclBCScript parameter
- Tcl Boundary Forces
- tclForces parameter
- Tcl Forces and Analysis
- tclForcesScript parameter
- Tcl Forces and Analysis
- tCouple parameter
- Temperature coupling parameters
- tCoupleCol parameter
- Temperature coupling parameters
- tCoupleFile parameter
- Temperature coupling parameters
- tCoupleTemp parameter
- Temperature coupling parameters
- TEMPAVG
- Standard output
- temperature parameter
- Initialization
- timestep parameter
- Timestep parameters
- TMD parameter
- Targeted Molecular Dynamics (TMD)
- TMDFile parameter
- Targeted Molecular Dynamics (TMD)
- TMDFinalRMSD parameter
- Targeted Molecular Dynamics (TMD)
- TMDFirstStep parameter
- Targeted Molecular Dynamics (TMD)
- TMDInitialRMSD parameter
- Targeted Molecular Dynamics (TMD)
- TMDk parameter
- Targeted Molecular Dynamics (TMD)
- TMDLastStep parameter
- Targeted Molecular Dynamics (TMD)
- TMDOutputFreq parameter
- Targeted Molecular Dynamics (TMD)
- topology psfgen command
- List of Commands
- TOTAL2 energy
- Standard output
- TOTAL3 energy
- Standard output
- twoAwayX
- Improving Parallel Scaling
- twoAwayY
- Improving Parallel Scaling
- twoAwayZ
- Improving Parallel Scaling
- units used for output
- Standard output
- useConstantArea parameter
- Pressure Control
- useConstantRatio parameter
- Pressure Control
- useFlexibleCell parameter
- Pressure Control
- useGroupPressure parameter
- Pressure Control
- useSettle parameter
- Bond constraint parameters
- vdwForceSwitching parameter
- Non-bonded force field parameters
- vdwGeometricSigma parameter
- Non-bonded force field parameters
- velDCDfile parameter
- Output files
- velDCDfreq parameter
- Output files
- velocities parameter
- Input files
- velocityQuenching parameter
- Velocity quenching parameters
- waterModel parameter
- Water model parameters
- wrapAll parameter
- Periodic boundary conditions
- wrapNearest parameter
- Periodic boundary conditions
- wrapWater parameter
- Periodic boundary conditions
- writepdb psfgen command
- List of Commands
- writepsf psfgen command
- List of Commands
- XSTfile parameter
- Periodic boundary conditions
- XSTfreq parameter
- Periodic boundary conditions
- zeroMomentum parameter
- Conserving momentum
namd@ks.uiuc.edu