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Contents
- 1-4scaling parameter
- Non-bonded force field parameters
- cphRun command
- New Commands and Keywords
- cphRun command
- New Commands and Keywords
- outputFreq colvars histogram keyword
- Multidimensional histograms
- outputFile colvars histogram keyword
- Multidimensional histograms
- outputFileDX colvars histogram keyword
- Multidimensional histograms
- gatherVectorColvars colvars histogram keyword
- Multidimensional histograms
- weights colvars histogram keyword
- Multidimensional histograms
- lowerBoundaries colvars histogramGrid keyword
- Grid definition for multidimensional
- abort command
- Tcl scripting interface and
- accelMD parameter
- NAMD parameters
- accelMDalpha parameter
- NAMD parameters
- accelMDdihe parameter
- NAMD parameters
- accelMDdual parameter
- NAMD parameters
- accelMDE parameter
- NAMD parameters
- accelMDFirstStep parameter
- NAMD parameters
- accelMDG parameter
- NAMD parameters
- accelMDGcMDPrepSteps parameter
- NAMD parameters
- accelMDGcMDSteps parameter
- NAMD parameters
- accelMDGEquiPrepSteps parameter
- NAMD parameters
- accelMDGEquiSteps parameter
- NAMD parameters
- accelMDGiE parameter
- NAMD parameters
- accelMDGRestart parameter
- NAMD parameters
- accelMDGRestartFile parameter
- NAMD parameters
- accelMDGSigma0D parameter
- NAMD parameters
- accelMDGSigma0P parameter
- NAMD parameters
- accelMDLastStep parameter
- NAMD parameters
- accelMDOutFreq parameter
- NAMD parameters
- accelMDTalpha parameter
- NAMD parameters
- accelMDTE parameter
- NAMD parameters
- acceptor colvars hBond keyword
- hBond: hydrogen bond between
- adaptTempBins parameter
- NAMD parameters
- adaptTempCgamma parameter
- NAMD parameters
- adaptTempDt parameter
- NAMD parameters
- adaptTempFirstStep parameter
- NAMD parameters
- adaptTempFreq parameter
- NAMD parameters
- adaptTempInFile parameter
- NAMD parameters
- adaptTempLangevin parameter
- NAMD parameters
- adaptTempLastStep parameter
- NAMD parameters
- adaptTempMD parameter
- NAMD parameters
- adaptTempOutFreq parameter
- NAMD parameters
- adaptTempRandom parameter
- NAMD parameters
- adaptTempRescaling parameter
- NAMD parameters
- adaptTempRestartFile parameter
- NAMD parameters
- adaptTempRestartFreq parameter
- NAMD parameters
- adaptTempTmax parameter
- NAMD parameters
- adaptTempTmin parameter
- NAMD parameters
- alch parameter
- Implementation of the free
- alchBondDecouple parameter
- Implementation of the free
- alchBondLambdaEnd parameter
- Implementation of the free
- 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
- Tcl scripting interface and
| Implementation of the free
- alchLambda2 parameter
- Tcl scripting interface and
| Implementation of the free
- alchLambdaIDWS 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
- alphaCutoff parameter
- Configuration Parameters
- amber parameter
- AMBER force field parameters
- ambercoor parameter
- AMBER force field parameters
- analysis colvars global keyword
- Configuration syntax for the
- angleRef colvars alpha keyword
- alpha: -helix content
- angleTol colvars alpha keyword
- alpha: -helix content
- applyBias colvars abf keyword
- Parameters for ABF
- atomNameResidueRange colvars atom group keyword
- Atom selection keywords
- atomNumbers colvars atom group keyword
- Atom selection keywords
- atomNumbersRange colvars atom group keyword
- Atom selection keywords
- atoms colvars cartesian keyword
- cartesian: vector of atomic
- atoms colvars polarPhi keyword
- polarTheta: polar angle in
- atoms colvars polarPhi keyword
- polarPhi: azimuthal angle in
- atoms colvars rmsd keyword
- rmsd: root mean square
- Atoms moving too fast
- Non-bonded interaction distance-testing
- atomsCol colvars atom group keyword
- Atom selection keywords
- atomsColValue colvars atom group keyword
- Atom selection keywords
- atomsFile colvars atom group keyword
- Atom selection keywords
- atomsOfGroup colvars atom group keyword
- Atom selection keywords
- auto psfgen command
- List of Commands
- axis colvars distanceZ keyword
- distanceZ: projection of a
- axis colvars inertiaZ keyword
- inertiaZ: total moment of
- axis colvars tilt keyword
- spinAngle: angle of rotation
- Bad global exclusion count
- Non-bonded interaction distance-testing
- BerendsenPressure parameter
- Tcl scripting interface and
| Berendsen pressure bath coupling
- BerendsenPressureCompressibility parameter
- Tcl scripting interface and
| Berendsen pressure bath coupling
- BerendsenPressureFreq parameter
- Berendsen pressure bath coupling
- BerendsenPressureRelaxationTime parameter
- Tcl scripting interface and
| Berendsen pressure bath coupling
- BerendsenPressureTarget parameter
- Tcl scripting interface and
| Berendsen pressure bath coupling
- biasTemperature colvars metadynamics keyword
- Well-tempered metadynamics
- binaryoutput parameter
- Tcl scripting interface and
| 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
- centerReference colvars atom group keyword
- Warning on rotating frames
- centers colvars harmonic keyword
- Harmonic restraints
- centers colvars linear keyword
- Linear restraints
- centers colvars alb keyword
- Adaptive Linear Bias/Experiment Directed
- checkpoint command
- Tcl scripting interface and
- checkpointFree command
- Tcl scripting interface and
| Multiple-copy/replica-exchange scripting interface
- checkpointLoad command
- Tcl scripting interface and
| Multiple-copy/replica-exchange scripting interface
- checkpointStore command
- Tcl scripting interface and
| Multiple-copy/replica-exchange scripting interface
- checkpointSwap command
- Tcl scripting interface and
| Multiple-copy/replica-exchange scripting interface
- closestToQuaternion colvars orientation keyword
- orientation: orientation from reference
- colvars colvars colvar bias keyword
- Biasing and analysis methods
- colvars colvars NAMD configuration file keyword
- NAMD parameters
- colvarsConfig colvars NAMD configuration file keyword
- NAMD parameters
- colvarsInput colvars NAMD configuration file keyword
- NAMD parameters
- colvarsRestartFrequency colvars global keyword
- Configuration syntax for the
- colvarsTrajFrequency colvars global keyword
- Configuration syntax for the
- COMmotion parameter
- Initialization
- componentCoeff colvars any component keyword
- Linear and polynomial combinations
- componentExp colvars any component keyword
- Linear and polynomial combinations
- consexp parameter
- Position restraint parameters
- consForceConfig command
- Tcl scripting interface and
| Constant Forces
- consForceFile parameter
- Constant Forces
- consForceScaling parameter
- Tcl scripting interface and
| Constant Forces
- conskcol parameter
- Position restraint parameters
- conskfile parameter
- Position restraint parameters
- consref parameter
- Position restraint parameters
- constantForce parameter
- Tcl scripting interface and
| Constant Forces
- constraints parameter
- Position restraint parameters
- constraintScaling parameter
- Tcl scripting interface and
| Position restraint parameters
- coord psfgen command
- List of Commands
- coordinates parameter
- Input files
- coordpdb psfgen command
- List of Commands
- coorfile command
- Tcl scripting interface and
- corrFunc colvars colvar keyword
- Statistical analysis of collective
- corrFuncLength colvars colvar keyword
- Statistical analysis of collective
- corrFuncNormalize colvars colvar keyword
- Statistical analysis of collective
- corrFuncOffset colvars colvar keyword
- Statistical analysis of collective
- corrFuncOutputFile colvars colvar keyword
- Statistical analysis of collective
- corrFuncStride colvars colvar keyword
- Statistical analysis of collective
- corrFuncType colvars colvar keyword
- Statistical analysis of collective
- corrFuncWithColvar colvars colvar keyword
- Statistical analysis of collective
- cosAngles parameter
- MARTINI Residue-Based Coarse-Grain Forcefield
- cphConfigFile parameter
- Required Keywords
- cphExcludeResidue parameter
- Commonly Used Options
- cphForceConstant parameter
- Specialized Options
- cphMaxProposalAttempts parameter
- Commonly Used Options
- cphMDBasename parameter
- Specialized Options
- cphNumMinSteps parameter
- Commonly Used Options
- cphNumstepsPerSwitch parameter
- Required Keywords
- cphOutFile parameter
- Commonly Used Options
- cphProposalWeight parameter
- Commonly Used Options
- cphRestartFile parameter
- Commonly Used Options
- cphRestartFreq parameter
- Commonly Used Options
- cphSetResiduepKai parameter
- Commonly Used Options
- cphSetResidueState parameter
- Commonly Used Options
- cphSWBasename parameter
- Specialized Options
- customFunction colvars colvar keyword
- Colvars as custom functions
- customFunctionType colvars colvar keyword
- Colvars as custom functions
- cutoff colvars coordNum keyword
- coordNum: coordination number between
- cutoff parameter
- Non-bonded force field parameters
- cutoff3 colvars coordNum keyword
- coordNum: coordination number between
- 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
- CZARestimator colvars abf keyword
- CZAR estimator of the
- dcdFile command
- Multiple-copy/replica-exchange scripting interface
- DCDfile parameter
- Tcl scripting interface and
| Output files
- DCDfreq parameter
- Output files
- DCDUnitCell parameter
- Output files
- delatom psfgen command
- List of Commands
- dielectric parameter
- Non-bonded force field parameters
- differenceVector colvars eigenvector keyword
- eigenvector: projection of the
- drude parameter
- Drude force field parameters
- drudeBondConst parameter
- Drude force field parameters
- drudeBondLen parameter
- Drude force field parameters
- drudeDamping parameter
- Drude force field parameters
- drudeNbTholeCut parameter
- Drude force field parameters
- drudeTemp parameter
- Drude force field parameters
- dummyAtom colvars atom group keyword
- Atom selection keywords
- dumpPartialFreeEnergyFile colvars metadynamics keyword
- Multiple-replicas metadynamics
- eField parameter
- Tcl scripting interface and
| External Electric Field
- eFieldFreq parameter
- Tcl scripting interface and
- eFieldNormalized parameter
- External Electric Field
- eFieldOn parameter
- External Electric Field
- eFieldPhase parameter
- Tcl scripting interface and
- enableFitGradients colvars atom group keyword
- Warning on rotating frames
- enableForces colvars atom group keyword
- Warning on rotating frames
- 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
- exit command
- Tcl scripting interface and
- expandBoundaries colvars colvar keyword
- General options for a
- expDenom colvars coordNum keyword
- coordNum: coordination number between
- expNumer colvars coordNum keyword
- coordNum: coordination number between
- exponent colvars distanceInv keyword
- distanceInv: mean distance between
- extCoordFilename parameter
- External Program Forces
- extendedFluctuation colvars colvar keyword
- Extended Lagrangian.
- extendedLagrangian colvars colvar keyword
- Extended Lagrangian.
- extendedLangevinDamping colvars colvar keyword
- Extended Lagrangian.
- extendedSystem parameter
- Periodic boundary conditions
- extendedTemp colvars colvar keyword
- Extended Lagrangian.
- extendedTimeConstant colvars colvar keyword
- Extended Lagrangian.
- 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
- fittingGroup colvars atom group keyword
- Warning on rotating frames
- fixedAtoms parameter
- Tcl scripting interface and
| Fixed atoms parameters
- fixedAtomsCol parameter
- Fixed atoms parameters
- fixedAtomsFile parameter
- Fixed atoms parameters
- fixedAtomsForces parameter
- Tcl scripting interface and
| Fixed atoms parameters
- forceConstant colvars harmonic keyword
- Harmonic restraints
- forceConstant colvars linear keyword
- Linear restraints
- forceConstant colvars histogramRestraint keyword
- Probability distribution-restraints
- forceDCDfile parameter
- Output files
- forceDCDfreq parameter
- Output files
- forceNoPBC colvars distance keyword
- distance: center-of-mass distance between
- forceRange colvars alb keyword
- Adaptive Linear Bias/Experiment Directed
- FullDirect parameter
- Full direct parameters
- fullElectFrequency parameter
- Multiple timestep parameters
- fullSamples colvars abf keyword
- Parameters for ABF
- gaussianSigma colvars histogramRestraint keyword
- Probability distribution-restraints
- GBIS parameter
- Configuration Parameters
- GBISBeta parameter
- Configuration Parameters
- GBISDelta parameter
- Configuration Parameters
- GBISGamma parameter
- Configuration Parameters
- GoCoordinates parameter
- Configuration file modifications
- GoForcesOn parameter
- Configuration file modifications
- GoMethod parameter
- Configuration file modifications
- GoParameters parameter
- Configuration file modifications
- GPRESSAVG
- Standard output
- GPRESSURE
- Standard output
- grocoorfile parameter
- GROMACS force field parameters
| Configuration file modifications
- gromacs parameter
- GROMACS force field parameters
| Configuration file modifications
- GromacsPair parameter
- Configuration file modifications
- grotopfile parameter
- GROMACS force field parameters
| Configuration file modifications
- group1 colvars distance keyword
- distance: center-of-mass distance between
- group2CenterOnly colvars coordNum keyword
- coordNum: coordination number between
- guesscoord psfgen command
- List of Commands
- hardLowerBoundary colvars colvar keyword
- General options for a
- hardUpperBoundary colvars colvar keyword
- General options for a
- hBondCoeff colvars alpha keyword
- alpha: -helix content
- hBondCutoff colvars alpha keyword
- alpha: -helix content
- hBondExpDenom colvars alpha keyword
- alpha: -helix content
- hBondExpNumer colvars alpha keyword
- alpha: -helix content
- hgroupCutoff (Å) parameter
- Non-bonded interaction distance-testing
- hideJacobian colvars abf keyword
- Parameters for ABF
- hillWeight colvars metadynamics keyword
- Metadynamics
- hillWidth colvars metadynamics keyword
- Metadynamics
- historyFreq colvars abf keyword
- 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)
- indexFile colvars global keyword
- Configuration syntax for the
- indexGroup colvars atom group keyword
- Atom selection keywords
- inputPrefix colvars abf keyword
- Parameters for ABF
- intrinsicRadiusOffset parameter
- Configuration Parameters
- ionConcentration parameter
- Configuration Parameters
- isset command
- Tcl scripting interface and
- istrue command
- Tcl scripting interface and
- keepFreeEnergyFiles colvars metadynamics keyword
- Output files
- keepHills colvars metadynamics keyword
- Compatibility and post-processing
- lambdaSchedule colvars harmonic keyword
- Changing force constant
- 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
- Tcl scripting interface and
| Nosé-Hoover Langevin piston pressure
- LangevinPistonDecay parameter
- Tcl scripting interface and
| Nosé-Hoover Langevin piston pressure
- LangevinPistonPeriod parameter
- Tcl scripting interface and
| Nosé-Hoover Langevin piston pressure
- LangevinPistonTarget parameter
- Tcl scripting interface and
| Nosé-Hoover Langevin piston pressure
- LangevinPistonTemp parameter
- Tcl scripting interface and
| Nosé-Hoover Langevin piston pressure
- langevinTemp parameter
- Tcl scripting interface and
| 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
- lowerBoundary colvars histogramRestraint keyword
- Probability distribution-restraints
- lowerBoundary colvars colvar keyword
- General options for a
- lowerWallConstant colvars harmonicWalls keyword
- Harmonic wall restraints
- lowerWalls colvars colvar keyword
- Harmonic wall restraints
- main colvars distanceZ keyword
- distanceZ: projection of a
- margin parameter
- Non-bonded interaction distance-testing
- margin violations
- Non-bonded interaction distance-testing
- martiniDielAllow parameter
- MARTINI Residue-Based Coarse-Grain Forcefield
- martiniSwitching parameter
- MARTINI Residue-Based Coarse-Grain Forcefield
- maxForce colvars abf keyword
- Parameters for ABF
- 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
- mgridforcelite 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
- move command
- Tcl scripting interface and
- movingConstraints parameter
- Moving Constraints
- movingConsVel parameter
- Moving Constraints
- MSM parameter
- MSM parameters
- MSMApprox parameter
- MSM parameters
- MSMBlockSizeX, MSMBlockSizeY, MSMBlockSizeZ parameter
- MSM parameters
- MSMGridSpacing parameter
- MSM parameters
- MSMLevels parameter
- MSM parameters
- MSMPadding parameter
- MSM parameters
- MSMQuality parameter
- MSM parameters
- MSMSerial parameter
- MSM parameters
- MSMSplit parameter
- MSM parameters
- MSMxmax, MSMymax, MSMzmax parameter
- MSM parameters
- MSMxmin, MSMymin, MSMzmin parameter
- MSM parameters
- MTSAlgorithm parameter
- Multiple timestep parameters
- multipleReplicas colvars metadynamics keyword
- Multiple-replicas metadynamics
- multiply psfgen command
- List of Commands
- mutate psfgen command
- List of Commands
- myReplica command
- Multiple-copy/replica-exchange scripting interface
- name colvars any component keyword
- Configuration keywords shared by
- name colvars colvar bias keyword
- Biasing and analysis methods
- name colvars metadynamics keyword
- Compatibility and post-processing
- name colvars colvar keyword
- General options for a
- name colvars atom group keyword
- Selecting atoms
- newHillFrequency colvars metadynamics keyword
- Metadynamics
- nonbondedFreq parameter
- Multiple timestep parameters
- nonbondedScaling parameter
- Tcl scripting interface and
| Non-bonded force field parameters
- numNodes command
- Tcl scripting interface and
- numPes command
- Tcl scripting interface and
- numPhysicalNodes command
- Tcl scripting interface and
- numReplicas command
- Multiple-copy/replica-exchange scripting interface
- numsteps parameter
- Timestep parameters
- oneSiteTotalForce colvars angle, dipoleAngle, dihedral keyword
- distance: center-of-mass distance between
- OPLS
- Non-bonded force field parameters
- output command
- Tcl scripting interface and
| Tcl scripting interface and
- output onlyforces command
- Tcl scripting interface and
- output withforces command
- Tcl scripting interface and
- outputAccumulatedWork colvars harmonic keyword
- Computing the work of
- outputAppliedForce colvars colvar keyword
- Trajectory output
- outputCenters colvars harmonic keyword
- Moving restraints: steered molecular
- outputEnergies parameter
- Standard output
- outputEnergy colvars colvar bias keyword
- Biasing and analysis methods
- outputEnergy colvars colvar keyword
- Trajectory output
- outputFreq colvars abf keyword
- Parameters for ABF
- outputMomenta parameter
- Standard output
- outputname parameter
- Output files
- outputPairlists parameter
- Non-bonded interaction distance-testing
- outputPressure parameter
- Standard output
- outputTiming parameter
- Standard output
- outputTotalForce colvars colvar keyword
- Trajectory output
- outputValue colvars colvar keyword
- Trajectory output
- outputVelocity colvars colvar keyword
- Trajectory 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
- pairListFrequency colvars coordNum keyword
- coordNum: coordination number between
- 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
- period colvars distanceZ, custom colvars keyword
- Periodic components.
- pH parameter
- Required Keywords
- 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 allcaps psfgen command
- List of Commands
- psfcontext create psfgen command
- List of Commands
- psfcontext delete psfgen command
- List of Commands
- psfcontext eval psfgen command
- List of Commands
- psfcontext mixedcase 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
- psfSegID colvars atom group keyword
- Atom selection keywords
- psfSegID colvars alpha keyword
- alpha: -helix content
- psfset psfgen command
- List of Commands
- python command
- Python scripting interface and
- 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
- rateMax colvars alb keyword
- Adaptive Linear Bias/Experiment Directed
- 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
- Tcl scripting interface and
| Temperature reassignment parameters
- rebinGrids colvars metadynamics keyword
- Performance tuning
- ref colvars distanceZ keyword
- distanceZ: projection of a
- ref2 colvars distanceZ keyword
- distanceZ: projection of a
- refHistogram colvars histogramRestraint keyword
- Probability distribution-restraints
- refHistogramFile colvars histogramRestraint keyword
- Probability distribution-restraints
- refPositions colvars atom group keyword
- Warning on rotating frames
- refPositions colvars rmsd keyword
- rmsd: root mean square
- refPositionsCol colvars atom group keyword
- Warning on rotating frames
- refPositionsCol colvars rmsd keyword
- rmsd: root mean square
- refPositionsColValue colvars atom group keyword
- Warning on rotating frames
- refPositionsColValue colvars rmsd keyword
- rmsd: root mean square
- refPositionsFile colvars atom group keyword
- Warning on rotating frames
- refPositionsFile colvars rmsd keyword
- rmsd: root mean square
- regenerate psfgen command
- List of Commands
| List of Commands
- reinitatoms command
- Tcl scripting interface and
- reinitvels command
- Tcl scripting interface and
- reloadCharges command
- Tcl scripting interface and
- replica exchange
- Replica exchange simulations
- replicaAtomRecv command
- Multiple-copy/replica-exchange scripting interface
- replicaAtomSend command
- Multiple-copy/replica-exchange scripting interface
- replicaAtomSendrecv command
- Multiple-copy/replica-exchange scripting interface
- replicaBarrier command
- Multiple-copy/replica-exchange scripting interface
- replicaDcdFile command
- Multiple-copy/replica-exchange scripting interface
- replicaEval command
- Multiple-copy/replica-exchange scripting interface
- replicaID colvars metadynamics keyword
- Multiple-replicas metadynamics
- replicaRecv command
- Multiple-copy/replica-exchange scripting interface
- replicaSend command
- Multiple-copy/replica-exchange scripting interface
- replicaSendrecv command
- Multiple-copy/replica-exchange scripting interface
- replicasRegistry colvars metadynamics keyword
- Multiple-replicas metadynamics
- replicaUniformPatchGrids parameter
- Multiple-copy/replica-exchange scripting interface
- replicaUpdateFrequency colvars metadynamics keyword
- Multiple-replicas metadynamics
- replicaYield command
- Multiple-copy/replica-exchange scripting interface
- rescaleFreq parameter
- Temperature rescaling parameters
- rescaleTemp parameter
- Tcl scripting interface and
| Temperature rescaling parameters
- rescalevels command
- Tcl scripting interface and
- resetpsf psfgen command
- List of Commands
- residue psfgen command
- List of Commands
- residueRange colvars alpha keyword
- alpha: -helix content
- restartfreq parameter
- Output files
- restartname parameter
- Tcl scripting interface and
| 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
- rotateReference colvars atom group keyword
- Warning on rotating frames
- rotConsAxis parameter
- Rotating Constraints
- rotConsPivot parameter
- Rotating Constraints
- rotConstraints parameter
- Rotating Constraints
- rotConsVel parameter
- Rotating Constraints
- run command
- Tcl scripting interface and
- run norepeat command
- Tcl scripting interface and
- runAve colvars colvar keyword
- Statistical analysis of collective
- runAveLength colvars colvar keyword
- Statistical analysis of collective
- runAveOutputFile colvars colvar keyword
- Statistical analysis of collective
- runAveStride colvars colvar keyword
- Statistical analysis of collective
- SASA parameter
- Configuration Parameters
- scalable colvars any component keyword
- Configuration keywords shared by
- scnb parameter
- AMBER force field parameters
- scriptedColvarForces colvars global keyword
- Scripted biases
- scriptedFunction colvars colvar keyword
- Colvars as scripted functions
- scriptedFunctionType colvars colvar keyword
- Colvars as scripted functions
- scriptedFunctionVectorSize colvars colvar keyword
- Colvars as scripted functions
- scriptingAfterBiases colvars global keyword
- Accessing biases
- seed parameter
- Initialization
- segment psfgen command
- List of Commands
- selectConstraints parameter
- Position restraint parameters
- selectConstrX parameter
- Position restraint parameters
- selectConstrY parameter
- Position restraint parameters
- selectConstrZ parameter
- Position restraint parameters
- shared colvars abf keyword
- Multiple-replica ABF
- sharedFreq colvars abf keyword
- Multiple-replica ABF
- SMD parameter
- Parameters
- SMDDir parameter
- Parameters
- SMDFile parameter
- Parameters
- SMDk parameter
- Parameters
- SMDk2 parameter
- Parameters
- SMDOutputFreq parameter
- Parameters
- SMDVel parameter
- Parameters
- smp colvars global keyword
- Configuration syntax for the
- solventDielectric parameter
- Configuration 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
- startup command
- Tcl scripting interface and
- staticAtomAssignment parameter
- Configuration file modifications
- stepspercycle parameter
- Non-bonded interaction distance-testing
- stochRescale parameter
- Stochastic velocity rescaling parameters
- stochRescaleFreq parameter
- Stochastic velocity rescaling parameters
- stochRescalePeriod parameter
- Stochastic velocity rescaling parameters
- stochRescaleTemp parameter
- Stochastic velocity rescaling parameters
- StrainRate parameter
- Nosé-Hoover Langevin piston pressure
- structure parameter
- Input files
- subtractAppliedForce colvars colvar keyword
- General options for a
- surfaceTension parameter
- Configuration Parameters
- SurfaceTensionTarget parameter
- Tcl scripting interface and
| Nosé-Hoover Langevin piston pressure
- switchdist parameter
- Non-bonded force field parameters
- switching parameter
- Non-bonded force field parameters
- symmetryFile parameter
- Symmetry Restraints
- symmetryFirstFullStep parameter
- Symmetry Restraints
- symmetryFirstStep parameter
- Symmetry Restraints
- symmetryk parameter
- Symmetry Restraints
- symmetrykFile parameter
- Symmetry Restraints
- symmetryLastFullStep parameter
- Symmetry Restraints
- symmetryLastStep parameter
- Symmetry Restraints
- symmetryMatrixFile parameter
- Symmetry Restraints
- symmetryRestraints parameter
- Symmetry Restraints
- symmetryScaleForces parameter
- Symmetry Restraints
- tableInterpType parameter
- Tabulated nonbonded interaction parameters
- tabulatedEnergies parameter
- Tabulated nonbonded interaction parameters
- tabulatedEnergiesFile parameter
- Tabulated nonbonded interaction parameters
- targetCenters colvars harmonic keyword
- Moving restraints: steered molecular
- targetEquilSteps colvars harmonic keyword
- Changing force constant
- targetForceConstant colvars harmonic keyword
- Changing force constant
- targetForceConstant colvars harmonicWalls keyword
- Harmonic wall restraints
- targetForceExponent colvars harmonic keyword
- Changing force constant
- targetNumStages colvars harmonic keyword
- Moving restraints: umbrella sampling
- targetNumSteps colvars harmonic keyword
- Moving restraints: steered molecular
- tcl.call() command
- Python scripting interface and
- tcl.eval() command
- Python scripting interface and
- 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)
- TMDDiffRMSD parameter
- Targeted Molecular Dynamics (TMD)
- TMDFile parameter
- Targeted Molecular Dynamics (TMD)
- TMDFile2 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)
- tolerance colvars coordNum keyword
- coordNum: coordination number between
- topology alias psfgen command
- List of Commands
- 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
- UIestimator colvars abf keyword
- Zheng/Yang estimator of the
- units used for output
- PDB files
| DCD trajectory files
| DCD trajectory files
| NAMD binary files
| Output files
| Standard output
- updateBias colvars abf keyword
- Parameters for ABF
- updateFrequency colvars alb keyword
- Adaptive Linear Bias/Experiment Directed
- updateGridforceScale parameter
- Tcl scripting interface and
| Grid Forces
- upperBoundary colvars colvar keyword
- General options for a
- upperWalls colvars colvar keyword
- Harmonic wall restraints
- useConstantArea parameter
- Tcl scripting interface and
| Pressure Control
- useConstantRatio parameter
- Tcl scripting interface and
| Pressure Control
- useFlexibleCell parameter
- Tcl scripting interface and
| Pressure Control
- useGrids colvars metadynamics keyword
- Performance tuning
- useGroupPressure parameter
- Tcl scripting interface and
| Pressure Control
- useSettle parameter
- Bond constraint parameters
- vdwForceSwitching parameter
- Non-bonded force field parameters
- vdwGeometricSigma parameter
- Non-bonded force field parameters
- vector colvars eigenvector keyword
- eigenvector: projection of the
- vectorCol colvars eigenvector keyword
- eigenvector: projection of the
- vectorColValue colvars eigenvector keyword
- eigenvector: projection of the
- vectorFile colvars dihedralPC keyword
- dihedralPC: protein dihedral pricipal
- vectorFile colvars eigenvector keyword
- eigenvector: projection of the
- vectorNumber colvars dihedralPC keyword
- dihedralPC: protein dihedral pricipal
- velDCDfile parameter
- Output files
- velDCDfreq parameter
- Output files
- velocities parameter
- Input files
- velocityQuenching parameter
- Velocity quenching parameters
- waterModel parameter
- Water Models
- wellTempered colvars metadynamics keyword
- Well-tempered metadynamics
- width colvars histogramRestraint keyword
- Probability distribution-restraints
- width colvars colvar keyword
- General options for a
- wrapAll parameter
- Periodic boundary conditions
- wrapAround colvars distanceZ, dihedral, spinAngle, custom colvars keyword
- Periodic components.
- wrapNearest parameter
- Periodic boundary conditions
- wrapWater parameter
- Periodic boundary conditions
- writeCZARwindowFile colvars abf keyword
- CZAR estimator of the
- writeFreeEnergyFile colvars metadynamics keyword
- Output files
- writeHillsTrajectory colvars metadynamics keyword
- Compatibility and post-processing
- writeHistogram colvars metadynamics keyword
- Probability distribution-restraints
- writenamdbin psfgen command
- List of Commands
- writepdb psfgen command
- List of Commands
- writepsf psfgen command
- List of Commands
- writeTIPMF colvars colvar bias keyword
- Biasing and analysis methods
- writeTISamples colvars colvar bias keyword
- Biasing and analysis methods
- XSTfile parameter
- Periodic boundary conditions
- XSTfreq parameter
- Periodic boundary conditions
- zeroMomentum parameter
- Conserving momentum
http://www.ks.uiuc.edu/Research/namd/