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Contents
- 1-4scaling parameter
- Basic dynamics
- abf command
- Parameters for ABF simulations
- 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 simulations
- Atoms moving too fast
- Nonbonded interaction distance-testing
- auto psfgen command
- List of Commands
- Bad global exclusion count
- Nonbonded 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
- Basic dynamics
- consexp parameter
- Harmonic constraint parameters
- consforcefile parameter
- Constant Forces
- conskcol parameter
- Harmonic constraint parameters
- conskfile parameter
- Harmonic constraint parameters
- consref parameter
- Harmonic constraint parameters
- constantforce parameter
- Constant Forces
- constraints parameter
- Harmonic constraint parameters
- constraintScaling parameter
- Harmonic constraint parameters
- coord psfgen command
- List of Commands
- coordinate parameter
- Parameters for ABF simulations
- coordinates parameter
- Input files
- coordpdb psfgen command
- List of Commands
- coorfile command
- Tcl scripting interface and
- cutoff parameter
- Simulation space partitioning
- 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
- Basic dynamics
- distFile parameter
- Parameters for ABF simulations
- dSmooth parameter
- Parameters for ABF simulations
- dxi parameter
- Parameters for ABF simulations
- eField parameter
- External Electric Field
- eFieldOn parameter
- External Electric Field
- error message
- Atoms moving too fast
- Nonbonded interaction distance-testing
- Bad global exclusion count
- Nonbonded interaction distance-testing
- exclude parameter
- Basic dynamics
- ExcludeFromPressure parameter
- Nosé-Hoover Langevin piston pressure
- ExcludeFromPressureCol parameter
- Nosé-Hoover Langevin piston pressure
- ExcludeFromPressureFile parameter
- Nosé-Hoover Langevin piston pressure
- extendedSystem parameter
- Periodic boundary conditions
- fep parameter
- Implementation of free energy
- fepCol parameter
- Implementation of free energy
- fepEquilSteps parameter
- Implementation of free energy
- fepFile parameter
- Implementation of free energy
- fepOutFile parameter
- Implementation of free energy
- fepOutFreq parameter
- Implementation of free energy
- 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
- FMA parameter
- DPMTA parameters
- FMAFFT parameter
- DPMTA parameters
- FMAFFTBlock parameter
- DPMTA parameters
- FMALevels parameter
- DPMTA parameters
- FMAMp parameter
- DPMTA parameters
- FMAtheta parameter
- DPMTA parameters
- fMax parameter
- Parameters for ABF simulations
- forceConst parameter
- Parameters for ABF simulations
- freeEnergy parameter
- Free Energy of Conformational
- freeEnergyConfig parameter
- Free Energy of Conformational
- FullDirect parameter
- Full direct parameters
- fullElectFrequency parameter
- Multiple timestep parameters
- fullSamples parameter
- Parameters for ABF simulations
- 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
- Simulation space partitioning
- historyFile parameter
- Parameters for ABF simulations
- 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)
- inFiles parameter
- Parameters for ABF simulations
- lambda parameter
- Implementation of free energy
- lambda2 parameter
- Implementation of free energy
- 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
- Simulation space partitioning
- longSplitting parameter
- Multiple timestep parameters
- margin parameter
- Simulation space partitioning
- margin violations
- Nonbonded interaction distance-testing
- maximumMove parameter
- Velocity quenching parameters
- measure command
- Tcl scripting interface and
- mergeCrossterms parameter
- Standard output
- 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
- moveBoundary parameter
- Parameters for ABF simulations
- 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
- numsteps parameter
- Timestep parameters
- OPLS
- Basic dynamics
- outFile parameter
- Parameters for ABF simulations
- output command
- Tcl scripting interface and
- outputEnergies parameter
- Standard output
- outputFreq parameter
- Parameters for ABF simulations
- outputMomenta parameter
- Standard output
- outputname parameter
- Output files
- outputPairlists parameter
- Simulation space partitioning
- 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
- Simulation space partitioning
- pairlistGrow parameter
- Simulation space partitioning
- pairlistMinProcs parameter
- Simulation space partitioning
- pairlistShrink parameter
- Simulation space partitioning
- pairlistsPerCycle parameter
- Simulation space partitioning
- pairlistTrigger parameter
- Simulation space partitioning
- 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
- 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
- restraintList parameter
- Parameters for ABF simulations
- rigidBonds parameter
- Basic dynamics
- rigidDieOnError parameter
- Basic dynamics
- rigidIterations parameter
- Basic dynamics
- rigidTolerance parameter
- Basic dynamics
- 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
- Basic dynamics
- segment psfgen command
- List of Commands
- selectConstraints parameter
- Harmonic constraint parameters
- selectConstrX parameter
- Harmonic constraint parameters
- selectConstrY parameter
- Harmonic constraint parameters
- selectConstrZ parameter
- Harmonic constraint 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
- Simulation space partitioning
- stepspercycle parameter
- Timestep parameters
- StrainRate parameter
- Nosé-Hoover Langevin piston pressure
- structure parameter
- Input files
- SurfaceTensionTarget parameter
- Nosé-Hoover Langevin piston pressure
- switchdist parameter
- Simulation space partitioning
- switching parameter
- Simulation space partitioning
- 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
- Basic dynamics
- 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
- useDPME parameter
- PME parameters
- useFlexibleCell parameter
- Pressure Control
- useGroupPressure parameter
- Pressure Control
- useSettle parameter
- Basic dynamics
- usMode parameter
- Parameters for ABF simulations
- vdwGeometricSigma parameter
- Basic dynamics
- velDCDfile parameter
- Output files
- velDCDfreq parameter
- Output files
- velocities parameter
- Input files
- velocityQuenching parameter
- Velocity quenching 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
- writeXiFreq parameter
- Parameters for ABF simulations
- xiMax parameter
- Parameters for ABF simulations
- xiMin parameter
- Parameters for ABF simulations
- XSTfile parameter
- Periodic boundary conditions
- XSTfreq parameter
- Periodic boundary conditions
- zeroMomentum parameter
- Basic dynamics
namd@ks.uiuc.edu