Index

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

Global keywords

angleRef colvars alpha keyword

alpha: $\alpha$ -helix content

angleTol colvars alpha keyword

alpha: $\alpha$ -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

Global keywords

colvarsTrajFrequency colvars global keyword

Global keywords

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

corrFuncLength colvars colvar keyword

Statistical analysis

corrFuncNormalize colvars colvar keyword

Statistical analysis

corrFuncOffset colvars colvar keyword

Statistical analysis

corrFuncOutputFile colvars colvar keyword

Statistical analysis

corrFuncStride colvars colvar keyword

Statistical analysis

corrFuncType colvars colvar keyword

Statistical analysis

corrFuncWithColvar colvars colvar keyword

Statistical analysis

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

Custom functions

customFunctionType colvars colvar keyword

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

Defining grid parameters

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

Defining grid parameters

hardUpperBoundary colvars colvar keyword

Defining grid parameters

hBondCoeff colvars alpha keyword

alpha: $\alpha$ -helix content

hBondCutoff colvars alpha keyword

alpha: $\alpha$ -helix content

hBondExpDenom colvars alpha keyword

alpha: $\alpha$ -helix content

hBondExpNumer colvars alpha keyword

alpha: $\alpha$ -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

Global keywords

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

Defining grid parameters

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 colvar bias keyword

Biasing and analysis methods

name colvars metadynamics keyword

Compatibility and post-processing

name colvars colvar keyword

Defining collective variables

name colvars any component keyword

Shared keywords for all

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 alpha keyword

alpha: $\alpha$ -helix content

psfSegID colvars atom group keyword

Atom selection keywords

psfset psfgen command

List of Commands

python command

Python scripting interface and

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 forceRAMD 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 namdVersion parameter

Random acceleration molecular dynamics

ramd ramdfilename parameter

Random acceleration molecular dynamics

ramd ramdSeed parameter

Random acceleration molecular dynamics

ramd ramdSteps 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: $\alpha$ -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

runAveLength colvars colvar keyword

Statistical analysis

runAveOutputFile colvars colvar keyword

Statistical analysis

runAveStride colvars colvar keyword

Statistical analysis

SASA parameter

Configuration Parameters

scalable colvars any component keyword

Shared keywords for all

scnb parameter

AMBER force field parameters

scriptedColvarForces colvars global keyword

Defining scripted biases

scriptedFunction colvars colvar keyword

Scripted functions

scriptedFunctionType colvars colvar keyword

Scripted functions

scriptedFunctionVectorSize colvars colvar keyword

Scripted functions

scriptingAfterBiases colvars global keyword

Performance of scripted 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

Global keywords

soluteScaling parameter

NAMD parameters

soluteScalingAll parameter

NAMD parameters

soluteScalingCol parameter

NAMD parameters

soluteScalingFactor parameter

NAMD parameters

soluteScalingFactorCharge parameter

NAMD parameters

soluteScalingFactorVdw parameter

NAMD parameters

soluteScalingFile parameter

NAMD parameters

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

Backward-compatibility

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

Defining grid parameters

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 eigenvector keyword

eigenvector: projection of the

vectorFile colvars dihedralPC keyword

dihedralPC: protein dihedral pricipal

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

Defining grid parameters

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