Index (NAMD 2.13 User's Guide)

New Commands and Keywords

cphRun command

cphRun command

New Commands and Keywords

outputFreq colvars histogram keyword

outputFile colvars histogram keyword

outputFileDX colvars histogram keyword

gatherVectorColvars colvars histogram keyword

weights colvars histogram keyword

Grid definition for multidimensional

lowerBoundaries colvars histogramGrid keyword

abf

colvars: Parameters for ABF
name: Parameters for ABF

alb

colvars: Adaptive Linear Bias/Experiment Directed
name: Adaptive Linear Bias/Experiment Directed

angle

forceNoPBC: angle: angle between three
group1: angle: angle between three
group2: angle: angle between three
group3: angle: angle between three
oneSiteTotalForce: angle: angle between three

coordNum

group1: coordNum: coordination number between
group2: coordNum: coordination number between

dihedral

forceNoPBC: dihedral: torsional angle between
group1: dihedral: torsional angle between
group2: dihedral: torsional angle between
group3: dihedral: torsional angle between
group4: dihedral: torsional angle between
oneSiteTotalForce: dihedral: torsional angle between

dihedralPC

psfSegID: dihedralPC: protein dihedral pricipal
residueRange: dihedralPC: protein dihedral pricipal

dipoleAngle

forceNoPBC: dipoleAngle: angle between two
group1: dipoleAngle: angle between two
group2: dipoleAngle: angle between two
group3: dipoleAngle: angle between two
oneSiteTotalForce: dipoleAngle: angle between two

distance

group2: distance: center-of-mass distance between

distanceDir

forceNoPBC: distanceDir: distance unit vector
group1: distanceDir: distance unit vector
group2: distanceDir: distance unit vector
oneSiteTotalForce: distanceDir: distance unit vector

distanceInv

group1: distanceInv: mean distance between
group2: distanceInv: mean distance between
oneSiteTotalForce: distanceInv: mean distance between

distancePairs

forceNoPBC: distancePairs: set of pairwise
group1: distancePairs: set of pairwise
group2: distancePairs: set of pairwise

distanceVec

forceNoPBC: distanceVec: distance vector between
group1: distanceVec: distance vector between
group2: distanceVec: distance vector between
oneSiteTotalForce: distanceVec: distance vector between

distanceXY

axis: distanceXY: modulus of the
forceNoPBC: distanceXY: modulus of the
main: distanceXY: modulus of the
ref2: distanceXY: modulus of the
ref: distanceXY: modulus of the

distanceZ

forceNoPBC: distanceZ: projection of a
oneSiteTotalForce: distanceZ: projection of a | distanceXY: modulus of the

eigenvector

atoms: eigenvector: projection of the
refPositions: eigenvector: projection of the
refPositionsCol: eigenvector: projection of the
refPositionsColValue: eigenvector: projection of the
refPositionsFile: eigenvector: projection of the

gyration

atoms: gyration: radius of gyration

harmonic

colvars: Harmonic restraints
name: Harmonic restraints
outputEnergy: Harmonic restraints
writeTIPMF: Harmonic restraints
writeTISamples: Harmonic restraints

harmonicWalls

colvars: Harmonic wall restraints
forceConstant: Harmonic wall restraints
lambdaSchedule: Harmonic wall restraints
name: Harmonic wall restraints
outputAccumulatedWork: Harmonic wall restraints
outputEnergy: Harmonic wall restraints
targetEquilSteps: Harmonic wall restraints
targetForceConstant: Harmonic wall restraints
targetForceExponent: Harmonic wall restraints
targetNumStages: Harmonic wall restraints
targetNumSteps: Harmonic wall restraints
upperWallConstant: Harmonic wall restraints
writeTIPMF: Harmonic wall restraints
writeTISamples: Harmonic wall restraints

hBond

cutoff: hBond: hydrogen bond between
donor: hBond: hydrogen bond between
expDenom: hBond: hydrogen bond between
expNumer: hBond: hydrogen bond between

histogram

colvars: Multidimensional histograms
name: Multidimensional histograms

histogramGrid

upperBoundaries: Grid definition for multidimensional
widths: Grid definition for multidimensional

histogramRestraint

colvars: Probability distribution-restraints
name: Probability distribution-restraints
outputEnergy: Probability distribution-restraints
upperBoundary: Probability distribution-restraints

inertia

atoms: inertia: total moment of

inertiaZ

atoms: inertiaZ: total moment of

linear

colvars: Linear restraints
lambdaSchedule: Linear restraints
name: Linear restraints
outputAccumulatedWork: Linear restraints
outputEnergy: Linear restraints
targetEquilSteps: Linear restraints
targetForceConstant: Linear restraints
targetForceExponent: Linear restraints
targetNumStages: Linear restraints
targetNumSteps: Linear restraints
writeTIPMF: Linear restraints
writeTISamples: Linear restraints

metadynamics

colvars: Basic syntax
name: Basic syntax
outputEnergy: Basic syntax
writeTIPMF: Basic syntax
writeTISamples: Basic syntax

orientation

atoms: orientation: orientation from reference
refPositions: orientation: orientation from reference
refPositionsCol: orientation: orientation from reference
refPositionsColValue: orientation: orientation from reference
refPositionsFile: orientation: orientation from reference

orientationAngle

atoms: orientationAngle: angle of rotation
refPositions: orientationAngle: angle of rotation
refPositionsCol: orientationAngle: angle of rotation
refPositionsColValue: orientationAngle: angle of rotation
refPositionsFile: orientationAngle: angle of rotation

orientationProj

atoms: orientationProj: cosine of the
refPositions: orientationProj: cosine of the
refPositionsCol: orientationProj: cosine of the
refPositionsColValue: orientationProj: cosine of the
refPositionsFile: orientationProj: cosine of the

selfCoordNum

cutoff3: selfCoordNum: coordination number between
cutoff: selfCoordNum: coordination number between
expDenom: selfCoordNum: coordination number between
expNumer: selfCoordNum: coordination number between
group1: selfCoordNum: coordination number between
pairListFrequency: selfCoordNum: coordination number between
tolerance: selfCoordNum: coordination number between

spinAngle

atoms: spinAngle: angle of rotation
refPositions: spinAngle: angle of rotation
refPositionsCol: spinAngle: angle of rotation
refPositionsColValue: spinAngle: angle of rotation
refPositionsFile: spinAngle: angle of rotation

tilt

atoms: tilt: cosine of the
axis: tilt: cosine of the
refPositions: tilt: cosine of the
refPositionsCol: tilt: cosine of the
refPositionsColValue: tilt: cosine of the
refPositionsFile: tilt: cosine of the

abort command

accelMD parameter

accelMDalpha parameter

accelMDdihe parameter

accelMDdual parameter

accelMDE parameter

accelMDFirstStep parameter

accelMDG parameter

accelMDGcMDPrepSteps parameter

accelMDGcMDSteps parameter

accelMDGEquiPrepSteps parameter

accelMDGEquiSteps parameter

accelMDGiE parameter

accelMDGRestart parameter

accelMDGRestartFile parameter

accelMDGSigma0D parameter

accelMDGSigma0P parameter

accelMDLastStep parameter

accelMDOutFreq parameter

accelMDTalpha parameter

accelMDTE parameter

hBond: hydrogen bond between

acceptor colvars hBond keyword

adaptTempBins parameter

adaptTempCgamma parameter

adaptTempDt parameter

adaptTempFirstStep parameter

adaptTempFreq parameter

adaptTempInFile parameter

adaptTempLangevin parameter

adaptTempLastStep parameter

adaptTempMD parameter

adaptTempOutFreq parameter

adaptTempRandom parameter

adaptTempRescaling parameter

adaptTempRestartFile parameter

adaptTempRestartFreq parameter

adaptTempTmax parameter

adaptTempTmin parameter

alch parameter

alchBondDecouple parameter

alchBondLambdaEnd parameter

alchCol parameter

alchDecouple parameter

alchElecLambdaStart parameter

alchEquilSteps parameter

alchFile parameter

Tcl scripting interface and | Implementation of the free

alchLambda parameter

alchLambda2 parameter

Tcl scripting interface and | Implementation of the free

alchLambdaIDWS parameter

alchOutFile parameter

alchOutFreq parameter

alchType parameter

alchVdwLambdaEnd parameter

alchVdwShiftCoeff parameter

alias psfgen command

List of Commands | List of Commands

alphaCutoff parameter

amber parameter

ambercoor parameter

analysis colvars global keyword

angleRef colvars alpha keyword

alpha: $\alpha$ -helix content

angleTol colvars alpha keyword

alpha: $\alpha$ -helix content

applyBias colvars abf keyword

atomNameResidueRange colvars atom group keyword

atomNumbers colvars atom group keyword

atomNumbersRange colvars atom group keyword

cartesian: vector of atomic

atoms colvars cartesian keyword

atoms colvars polarPhi keyword

polarTheta: polar angle in

atoms colvars polarPhi keyword

polarPhi: azimuthal angle in

atoms colvars rmsd keyword

Atoms moving too fast

atomsCol colvars atom group keyword

atomsColValue colvars atom group keyword

atomsFile colvars atom group keyword

atomsOfGroup colvars atom group keyword

auto psfgen command

axis colvars distanceZ keyword

spinAngle: angle of rotation

axis colvars inertiaZ keyword

inertiaZ: total moment of

axis colvars tilt keyword

Bad global exclusion count

Tcl scripting interface and | Berendsen pressure bath coupling

BerendsenPressure parameter

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

bincoordinates parameter

binvelocities parameter

bondedCUDA parameter

BOUNDARY energy

callback command

cellBasisVector1 parameter

cellBasisVector2 parameter

cellBasisVector3 parameter

cellOrigin parameter

centerReference colvars atom group keyword

centers colvars harmonic keyword

Harmonic restraints

centers colvars linear keyword

Linear restraints

centers colvars alb keyword

checkpoint command

Tcl scripting interface and | Multiple-copy/replica-exchange scripting interface

checkpointFree command

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

colvars colvars NAMD configuration file keyword

colvarsConfig colvars NAMD configuration file keyword

colvarsInput colvars NAMD configuration file keyword

colvarsRestartFrequency colvars global keyword

colvarsTrajFrequency colvars global keyword

Linear and polynomial combinations

COMmotion parameter

Initialization

componentCoeff colvars any component keyword

componentExp colvars any component keyword

Linear and polynomial combinations

consexp parameter

consForceConfig command

Tcl scripting interface and | Constant Forces

consForceFile parameter

Constant Forces

consForceScaling parameter

Tcl scripting interface and | Constant Forces

conskcol parameter

conskfile parameter

consref parameter

constantForce parameter

Tcl scripting interface and | Constant Forces

constraints parameter

Tcl scripting interface and | Position restraint parameters

constraintScaling parameter

coord psfgen command

coordinates parameter

coordpdb psfgen command

coorfile command

corrFunc colvars colvar keyword

corrFuncLength colvars colvar keyword

corrFuncNormalize colvars colvar keyword

corrFuncOffset colvars colvar keyword

corrFuncOutputFile colvars colvar keyword

corrFuncStride colvars colvar keyword

corrFuncType colvars colvar keyword

corrFuncWithColvar colvars colvar keyword

MARTINI Residue-Based Coarse-Grain Forcefield

cosAngles parameter

cphConfigFile parameter

Required Keywords

cphExcludeResidue parameter

cphForceConstant parameter

Specialized Options

cphMaxProposalAttempts parameter

cphMDBasename parameter

Specialized Options

cphNumMinSteps parameter

cphNumstepsPerSwitch parameter

Required Keywords

cphOutFile parameter

cphProposalWeight parameter

cphRestartFile parameter

cphRestartFreq parameter

cphSetResiduepKai parameter

cphSetResidueState parameter

cphSWBasename parameter

Specialized Options

customFunction colvars colvar keyword

Custom functions

customFunctionType colvars colvar keyword

Custom functions

cutoff colvars coordNum keyword

cutoff parameter

cutoff3 colvars coordNum keyword

cwd parameter

cylindricalBC parameter

cylindricalBCAxis parameter

cylindricalBCCenter parameter

cylindricalBCexp1 parameter

cylindricalBCexp2 parameter

cylindricalBCk1 parameter

cylindricalBCk2 parameter

cylindricalBCl1 parameter

cylindricalBCl2 parameter

cylindricalBCr1 parameter

cylindricalBCr2 parameter

CZARestimator colvars abf keyword

CZAR estimator of the

dcdFile command

DCDfile parameter

Tcl scripting interface and | Output files

DCDfreq parameter

DCDUnitCell parameter

delatom psfgen command

dielectric parameter

differenceVector colvars eigenvector keyword

drude parameter

drudeBondConst parameter

drudeBondLen parameter

drudeDamping parameter

drudeNbTholeCut parameter

drudeTemp parameter

dummyAtom colvars atom group keyword

dumpPartialFreeEnergyFile colvars metadynamics keyword

Tcl scripting interface and | External Electric Field

eField parameter

eFieldFreq parameter

eFieldNormalized parameter

External Electric Field

eFieldOn parameter

External Electric Field

eFieldPhase parameter

enableFitGradients colvars atom group keyword

enableForces colvars atom group keyword

error message

Atoms moving too fast: Non-bonded interaction distance-testing
Bad global exclusion count: Non-bonded interaction distance-testing

exclude parameter

ExcludeFromPressure parameter

ExcludeFromPressureCol parameter

ExcludeFromPressureFile parameter

exit command

expandBoundaries colvars colvar keyword

expDenom colvars coordNum keyword

expNumer colvars coordNum keyword

distanceInv: mean distance between

exponent colvars distanceInv keyword

extCoordFilename parameter

extendedFluctuation colvars colvar keyword

extendedLagrangian colvars colvar keyword

extendedLangevinDamping colvars colvar keyword

extendedSystem parameter

extendedTemp colvars colvar keyword

extendedTimeConstant colvars colvar keyword

extForceFilename parameter

extForces parameter

extForcesCommand parameter

extraBonds parameter

Extra bond, angle, and

extraBondsCosAngles parameter

Extra bond, angle, and

extraBondsFile parameter

Extra bond, angle, and

FFTWEstimate parameter

FFTWUseWisdom parameter

FFTWWisdomFile parameter

first psfgen command

firsttimestep parameter

Timestep parameters

fittingGroup colvars atom group keyword

Tcl scripting interface and | Fixed atoms parameters

fixedAtoms parameter

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

forceDCDfile parameter

forceDCDfreq parameter

distance: center-of-mass distance between

forceNoPBC colvars distance keyword

forceRange colvars alb keyword

FullDirect parameter

Full direct parameters

fullElectFrequency parameter

fullSamples colvars abf keyword

gaussianSigma colvars histogramRestraint keyword

GBIS parameter

GBISBeta parameter

GBISDelta parameter

GBISGamma parameter

GoCoordinates parameter

GoForcesOn parameter

GoMethod parameter

GoParameters parameter

GPRESSAVG

GPRESSURE

GROMACS force field parameters | Configuration file modifications

grocoorfile parameter

gromacs parameter

GROMACS force field parameters | Configuration file modifications

GromacsPair parameter

GROMACS force field parameters | Configuration file modifications

grotopfile parameter

group1 colvars distance keyword

distance: center-of-mass distance between

group2CenterOnly colvars coordNum keyword

guesscoord psfgen command

hardLowerBoundary colvars colvar keyword

hardUpperBoundary colvars colvar keyword

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

hideJacobian colvars abf keyword

hillWeight colvars metadynamics keyword

Basic syntax

hillWidth colvars metadynamics keyword

Basic syntax

historyFreq colvars abf keyword

IMDfreq parameter

IMDignore parameter

IMDon parameter

IMDport parameter

IMDwait parameter

indexFile colvars global keyword

indexGroup colvars atom group keyword

inputPrefix colvars abf keyword

intrinsicRadiusOffset parameter

ionConcentration parameter

isset command

istrue command

keepFreeEnergyFiles colvars metadynamics keyword

Compatibility and post-processing

keepHills colvars metadynamics keyword

lambdaSchedule colvars harmonic keyword

langevin parameter

langevinCol parameter

langevinDamping parameter

langevinFile parameter

langevinHydrogen parameter

Tcl scripting interface and | Nosé-Hoover Langevin piston pressure

LangevinPiston parameter

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

les parameter

lesCol parameter

lesFactor parameter

lesFile parameter

lesReduceMass parameter

lesReduceTemp parameter

limitdist parameter

LJcorrection parameter

longSplitting parameter

loweAndersen parameter

loweAndersenCutoff parameter

loweAndersenRate parameter

loweAndersenTemp parameter

lowerBoundary colvars histogramRestraint keyword

lowerBoundary colvars colvar keyword

lowerWallConstant colvars harmonicWalls keyword

lowerWalls colvars colvar keyword

main colvars distanceZ keyword

margin parameter

margin violations

MARTINI Residue-Based Coarse-Grain Forcefield

martiniDielAllow parameter

martiniSwitching parameter

MARTINI Residue-Based Coarse-Grain Forcefield

maxForce colvars abf keyword

Velocity quenching parameters

maximumMove parameter

measure command

mergeCrossterms parameter

mgridforce parameter

mgridforcechargecol parameter

mgridforcecol parameter

mgridforcecont1 parameter

mgridforcecont2 parameter

mgridforcecont3 parameter

mgridforcefile parameter

mgridforcelite parameter

mgridforcepotfile parameter

mgridforcescale parameter

mgridforcevoff parameter

mgridforcevolts parameter

minBabyStep parameter

minimization parameter

minimize command

minLineGoal parameter

minTinyStep parameter

MISC energy

molly parameter

mollyIterations parameter

mollyTolerance parameter

move command

movingConstraints parameter

Moving Constraints

movingConsVel parameter

Moving Constraints

MSM parameter

MSMApprox parameter

MSMBlockSizeX, MSMBlockSizeY, MSMBlockSizeZ parameter

MSMGridSpacing parameter

MSMLevels parameter

MSMPadding parameter

MSMQuality parameter

MSMSerial parameter

MSMSplit parameter

MSMxmax, MSMymax, MSMzmax parameter

MSMxmin, MSMymin, MSMzmin parameter

MTSAlgorithm parameter

multipleReplicas colvars metadynamics keyword

multiply psfgen command

mutate psfgen command

myReplica command

name colvars colvar bias keyword

Compatibility and post-processing

name colvars metadynamics keyword

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

Basic syntax

nonbondedFreq parameter

Tcl scripting interface and | Non-bonded force field parameters

nonbondedScaling parameter

numNodes command

numPes command

numPhysicalNodes command

numReplicas command

distance: center-of-mass distance between

numsteps parameter

Timestep parameters

oneSiteTotalForce colvars angle, dipoleAngle, dihedral keyword

OPLS

Tcl scripting interface and | Tcl scripting interface and

output command

output onlyforces command

output withforces command

outputAccumulatedWork colvars harmonic keyword

Computing the work of

outputAppliedForce colvars colvar keyword

Moving restraints: steered molecular

outputCenters colvars harmonic keyword

outputEnergies parameter

outputEnergy colvars colvar bias keyword

outputEnergy colvars colvar keyword

outputFreq colvars abf keyword

outputMomenta parameter

outputname parameter

outputPairlists parameter

outputPressure parameter

outputTiming parameter

outputTotalForce colvars colvar keyword

outputValue colvars colvar keyword

outputVelocity colvars colvar keyword

pairInteraction parameter

pairInteractionCol parameter

pairInteractionFile parameter

pairInteractionGroup1 parameter

pairInteractionGroup2 parameter

pairInteractionSelf parameter

pairlistdist parameter

pairListFrequency colvars coordNum keyword

pairlistGrow parameter

pairlistMinProcs parameter

pairlistShrink parameter

pairlistsPerCycle parameter

pairlistTrigger parameter

parameters parameter

paraTypeCharmm parameter

paraTypeXplor parameter

parmfile parameter

patch psfgen command

pdb psfgen command

pdbalias atom psfgen command

pdbalias residue psfgen command

period colvars distanceZ, custom colvars keyword

Periodic components

pH parameter

Required Keywords

PME parameter

PMEGridSizeX parameter

PMEGridSizeY parameter

PMEGridSizeZ parameter

PMEGridSpacing parameter

PMEInterpOrder parameter

PMEoffload parameter

PMEProcessors parameter

PMETolerance parameter

PRESSAVG

pressureProfile parameter

pressureProfileAtomTypes parameter

pressureProfileAtomTypesCol parameter

pressureProfileAtomTypesFile parameter

pressureProfileEwald parameter

pressureProfileEwaldX parameter

pressureProfileEwaldY parameter

pressureProfileEwaldZ parameter

pressureProfileFreq parameter

pressureProfileSlabs parameter

print command

psfcontext allcaps psfgen command

psfcontext create psfgen command

psfcontext delete psfgen command

psfcontext eval psfgen command

psfcontext mixedcase psfgen command

psfcontext psfgen command

psfcontext reset psfgen command

psfcontext stats psfgen command

psfSegID colvars alpha keyword

alpha: $\alpha$ -helix content

psfSegID colvars atom group keyword

psfset psfgen command

Python scripting interface and

python command

qmBaseDir parameter

qmBondColumn parameter

qmBondDist parameter

qmBondScheme parameter

qmBondValueType parameter

qmCharge parameter

qmChargeFromPSF parameter

qmChargeMode parameter

qmColumn parameter

qmConfigLine parameter

qmCSMD parameter

qmCSMDFile parameter

qmCustomPCFile parameter

qmCustomPCSelection parameter

qmElecEmbed parameter

qmEnergyStride parameter

qmExecPath parameter

qmForces parameter

qmLinkElement parameter

qmLiveSolventSel parameter

qmLSSFreq parameter

qmLSSMode parameter

qmLSSRef parameter

qmLSSResname parameter

qmMult parameter

qmOutStride parameter

qmParamPDB parameter

qmPCStride parameter

qmPointChargeScheme parameter

qmPositionOutStride parameter

qmPrepProc parameter

qmReplaceAll parameter

qmSecProc parameter

qmSimsPerNode parameter

qmSoftware parameter

qmSwitching parameter

qmSwitchingType parameter

qmVdwParams parameter

ramd debugLevel parameter

ramd firstProtAtom parameter

ramd firstRamdAtom parameter

ramd forceOutFreq parameter

ramd forceRAMD parameter

ramd lastProtAtom parameter

ramd lastRamdAtom parameter

ramd maxDist parameter

ramd namdVersion parameter

ramd ramdfilename parameter

ramd ramdSeed parameter

ramd ramdSteps parameter

ramd rMinRamd parameter

rateMax colvars alb keyword

readexclusions parameter

readpsf psfgen command

Temperature reassignment parameters

reassignFreq parameter

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

ref2 colvars distanceZ keyword

refHistogram colvars histogramRestraint keyword

refHistogramFile colvars histogramRestraint keyword

refPositions colvars atom group keyword

refPositions colvars rmsd keyword

refPositionsCol colvars atom group keyword

refPositionsCol colvars rmsd keyword

refPositionsColValue colvars atom group keyword

refPositionsColValue colvars rmsd keyword

refPositionsFile colvars atom group keyword

refPositionsFile colvars rmsd keyword

regenerate psfgen command

List of Commands | List of Commands

reinitatoms command

reinitvels command

reloadCharges command

Replica exchange simulations

replica exchange

replicaAtomRecv command

replicaAtomSend command

replicaAtomSendrecv command

replicaBarrier command

replicaDcdFile command

replicaEval command

replicaID colvars metadynamics keyword

replicaRecv command

replicaSend command

replicaSendrecv command

replicasRegistry colvars metadynamics keyword

replicaUniformPatchGrids parameter

replicaUpdateFrequency colvars metadynamics keyword

replicaYield command

Temperature rescaling parameters

rescaleFreq parameter

rescaleTemp parameter

Tcl scripting interface and | Temperature rescaling parameters

rescalevels command

resetpsf psfgen command

residue psfgen command

residueRange colvars alpha keyword

alpha: $\alpha$ -helix content

restartfreq parameter

restartname parameter

Tcl scripting interface and | Output files

restartsave parameter

rigidBonds parameter

rigidDieOnError parameter

rigidIterations parameter

rigidTolerance parameter

rotateReference colvars atom group keyword

rotConsAxis parameter

rotConsPivot parameter

rotConstraints parameter

rotConsVel parameter

run command

run norepeat command

runAve colvars colvar keyword

runAveLength colvars colvar keyword

runAveOutputFile colvars colvar keyword

runAveStride colvars colvar keyword

SASA parameter

scalable colvars any component keyword

Shared keywords for all

scnb parameter

Performance of scripted biases

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

seed parameter

Initialization

segment psfgen command

selectConstraints parameter

selectConstrX parameter

selectConstrY parameter

selectConstrZ parameter

shared colvars abf keyword

Multiple-replica ABF

sharedFreq colvars abf keyword

Multiple-replica ABF

SMD parameter

SMDDir parameter

SMDFile parameter

SMDk parameter

SMDk2 parameter

SMDOutputFreq parameter

SMDVel parameter

smp colvars global keyword

soluteScaling parameter

soluteScalingAll parameter

soluteScalingCol parameter

soluteScalingFactor parameter

soluteScalingFactorCharge parameter

soluteScalingFactorVdw parameter

soluteScalingFile parameter

solventDielectric parameter

source command

sphericalBC parameter

sphericalBCCenter parameter

sphericalBCexp1 parameter

sphericalBCexp2 parameter

sphericalBCk1 parameter

sphericalBCk2 parameter

sphericalBCr1 parameter

sphericalBCr2 parameter

splitPatch parameter

startup command

staticAtomAssignment parameter

stepspercycle parameter

stochRescale parameter

stochRescaleFreq parameter

stochRescaleHeat parameter

stochRescalePeriod parameter

stochRescaleTemp parameter

StrainRate parameter

structure parameter

subtractAppliedForce colvars colvar keyword

Backward-compatibility

surfaceTension parameter

Tcl scripting interface and | Nosé-Hoover Langevin piston pressure

SurfaceTensionTarget parameter

switchdist parameter

switching parameter

symmetryFile parameter

symmetryFirstFullStep parameter

symmetryFirstStep parameter

symmetryk parameter

symmetrykFile parameter

symmetryLastFullStep parameter

symmetryLastStep parameter

symmetryMatrixFile parameter

symmetryRestraints parameter

symmetryScaleForces parameter

Tabulated nonbonded interaction parameters

tableInterpType parameter

tabulatedEnergies parameter

Tabulated nonbonded interaction parameters

tabulatedEnergiesFile parameter

Tabulated nonbonded interaction parameters

targetCenters colvars harmonic keyword

Moving restraints: steered molecular

targetEquilSteps colvars harmonic keyword

targetForceConstant colvars harmonic keyword

targetForceConstant colvars harmonicWalls keyword

targetForceExponent colvars harmonic keyword

Moving restraints: umbrella sampling

targetNumStages colvars harmonic keyword

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

tCoupleCol parameter

tCoupleFile parameter

tCoupleTemp parameter

TEMPAVG

temperature parameter

Initialization

timestep parameter

Timestep parameters

TMD parameter

TMDDiffRMSD parameter

TMDFile parameter

TMDFile2 parameter

TMDFinalRMSD parameter

TMDFirstStep parameter

TMDInitialRMSD parameter

TMDk parameter

TMDLastStep parameter

TMDOutputFreq parameter

tolerance colvars coordNum keyword

topology alias psfgen command

topology psfgen command

TOTAL2 energy

TOTAL3 energy

Improving Parallel Scaling

twoAwayX

twoAwayY

Improving Parallel Scaling

twoAwayZ

Improving Parallel Scaling

UIestimator colvars abf keyword

Zheng/Yang estimator of the

units used for output

updateBias colvars abf keyword

updateFrequency colvars alb keyword

updateGridforceScale parameter

Tcl scripting interface and | Grid Forces

upperBoundary colvars colvar keyword

upperWalls colvars colvar keyword

useConstantArea parameter

useConstantRatio parameter

useFlexibleCell parameter

useGrids colvars metadynamics keyword

Performance tuning

useGroupPressure parameter

usePMECUDA parameter

useSettle parameter

vdwForceSwitching parameter

vdwGeometricSigma parameter

vector colvars eigenvector keyword

vectorCol colvars eigenvector keyword

vectorColValue colvars eigenvector keyword

vectorFile colvars eigenvector keyword

dihedralPC: protein dihedral pricipal

vectorFile colvars dihedralPC keyword

vectorNumber colvars dihedralPC keyword

dihedralPC: protein dihedral pricipal

velDCDfile parameter

velDCDfreq parameter

velocities parameter

Velocity quenching parameters

velocityQuenching parameter

waterModel parameter

Water Models

wellTempered colvars metadynamics keyword

Well-tempered metadynamics

width colvars histogramRestraint keyword

width colvars colvar keyword

wrapAll parameter

wrapAround colvars distanceZ, dihedral, spinAngle, custom colvars keyword

Periodic components

wrapNearest parameter

wrapWater parameter

writeCZARwindowFile colvars abf keyword

CZAR estimator of the

writeFreeEnergyFile colvars metadynamics keyword

Compatibility and post-processing

writeHillsTrajectory colvars metadynamics keyword

writeHistogram colvars metadynamics keyword

writenamdbin psfgen command

writepdb psfgen command

writepsf psfgen command

writeTIPMF colvars colvar bias keyword

writeTISamples colvars colvar bias keyword

XSTfile parameter

XSTfreq parameter