Index (NAMD 2.12b1 User's Guide)

Probability distribution-restraints | Probability distribution-restraints

< colvars t keyword

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

abort command

accelMD parameter

accelMDalpha parameter

accelMDdihe parameter

accelMDdual parameter

accelMDE parameter

accelMDFirstStep parameter

accelMDLastStep parameter

accelMDOutFreq parameter

accelMDTalpha parameter

accelMDTE parameter

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

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

angleRef colvars dihedralPC keyword

angleTol colvars alpha keyword

alpha: $\alpha$ -helix content

angleTol colvars dihedralPC keyword

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 rmsd keyword

atoms colvars eigenvector keyword

gyration: radius of gyration

atoms colvars gyration keyword

atoms colvars inertia keyword

inertia: total moment of

atoms colvars inertiaZ keyword

inertiaZ: total moment of

atoms colvars orientation keyword

atoms colvars orientationAngle keyword

atoms colvars orientationProj keyword

atoms colvars spinAngle keyword

atoms colvars tilt keyword

Atoms moving too fast

atomsCol colvars atom group keyword

atomsColValue colvars atom group keyword

atomsFile colvars atom group keyword

auto psfgen command

axis colvars distanceZ keyword

axis colvars inertiaZ keyword

inertiaZ: total moment of

axis colvars tilt keyword

axis colvars distanceXY keyword

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

BOUNDARY energy

callback command

cellBasisVector1 parameter

cellBasisVector2 parameter

cellBasisVector3 parameter

cellOrigin parameter

centerReference colvars atom group keyword

centers colvars harmonic keyword

centers colvars linear keyword

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

Biasing and analysis methods

colvars colvars colvar bias keyword

colvars colvars NAMD configuration file keyword

colvars colvars abf keyword

colvars colvars alb keyword

colvars colvars harmonic keyword

colvars colvars histogram keyword

colvars colvars histogramRestraint keyword

colvars colvars linear keyword

colvars colvars metadynamics keyword

colvarsConfig colvars NAMD configuration file keyword

colvarsInput colvars NAMD configuration file keyword

colvarsRestartFrequency colvars global keyword

colvarsTrajAppend 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 | Harmonic 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

cutoff colvars coordNum keyword

cutoff colvars hBond keyword

cutoff colvars selfCoordNum keyword

cutoff parameter

cutoff3 colvars coordNum keyword

cutoff3 colvars selfCoordNum 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

dcdFile command

DCDfile parameter

Tcl scripting interface and | Output files

DCDfreq parameter

DCDUnitCell parameter

delatom psfgen command

dielectric parameter

differenceVector colvars eigenvector keyword

donor colvars hBond 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

expDenom colvars hBond keyword

expDenom colvars selfCoordNum keyword

expNumer colvars coordNum keyword

expNumer colvars hBond keyword

expNumer colvars selfCoordNum 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

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

forceConstant colvars linear keyword

forceConstant colvars histogramRestraint keyword

forceDCDfile parameter

forceDCDfreq parameter

forceNoPBC colvars distance keyword

distancePairs: set of pairwise

forceNoPBC colvars distanceInv keyword

forceNoPBC colvars distanceZ keyword

distanceZ: projection of a | distanceXY: modulus of the

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

group1 colvars angle keyword

group1 colvars coordNum keyword

group1 colvars dihedral keyword

group1 colvars dipoleAngle keyword

distanceDir: distance unit vector

group1 colvars distanceDir keyword

group1 colvars distanceInv keyword

distanceInv: mean distance between | distancePairs: set of pairwise

group1 colvars distanceVec keyword

distanceVec: distance vector between

group1 colvars selfCoordNum keyword

group2 colvars angle keyword

group2 colvars coordNum keyword

group2 colvars dihedral keyword

group2 colvars dipoleAngle keyword

group2 colvars distance keyword

distanceDir: distance unit vector

group2 colvars distanceDir keyword

group2 colvars distanceInv keyword

distanceInv: mean distance between | distancePairs: set of pairwise

group2 colvars distanceVec keyword

distanceVec: distance vector between

group2 colvars selfCoordNum keyword

group2CenterOnly colvars coordNum keyword

group3 colvars angle keyword

group3 colvars dihedral keyword

group3 colvars dipoleAngle keyword

group4 colvars dihedral keyword

guesscoord psfgen command

hardLowerBoundary colvars colvar keyword

hardUpperBoundary colvars colvar keyword

hBondCoeff colvars alpha keyword

alpha: $\alpha$ -helix content

hBondCoeff colvars dihedralPC keyword

hBondCutoff colvars alpha keyword

alpha: $\alpha$ -helix content

hBondCutoff colvars dihedralPC keyword

hBondExpDenom colvars alpha keyword

alpha: $\alpha$ -helix content

hBondExpDenom colvars dihedralPC keyword

hBondExpNumer colvars alpha keyword

alpha: $\alpha$ -helix content

hBondExpNumer colvars dihedralPC keyword

hgroupCutoff (Å) parameter

hideJacobian colvars abf keyword

hillWeight colvars metadynamics keyword

hillWidth colvars metadynamics keyword

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 colvar keyword

lowerWall colvars colvar keyword

lowerWallConstant colvars colvar keyword

main colvars distanceZ keyword

main colvars distanceXY 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

Configuration keywords shared by

name colvars any component keyword

name colvars colvar bias keyword

Biasing and analysis methods

name colvars metadynamics keyword

Compatibility and post-processing

name colvars colvar keyword

name colvars abf keyword

name colvars alb keyword

name colvars harmonic keyword

name colvars histogram keyword

name colvars histogramRestraint keyword

name colvars linear keyword

name colvars metadynamics keyword

newHillFrequency colvars metadynamics keyword

nonbondedFreq parameter

Tcl scripting interface and | Non-bonded force field parameters

nonbondedScaling parameter

numNodes command

numPes command

numPhysicalNodes command

numReplicas command

numsteps parameter

Timestep parameters

oneSiteTotalForce colvars angle, dipoleAngle, dihedral keyword

oneSiteTotalForce colvars angle keyword

oneSiteTotalForce colvars dihedral keyword

oneSiteTotalForce colvars dipoleAngle keyword

distanceDir: distance unit vector

oneSiteTotalForce colvars distanceDir keyword

oneSiteTotalForce colvars distanceInv keyword

distanceInv: mean distance between

oneSiteTotalForce colvars distanceVec keyword

distanceVec: distance vector between

oneSiteTotalForce colvars distanceZ keyword

distanceZ: projection of a | distanceXY: modulus of the

OPLS

Tcl scripting interface and | Tcl scripting interface and

output command

output onlyforces command

output withforces command

outputAccumulatedWork colvars harmonic keyword

outputAppliedForce colvars colvar keyword

outputCenters colvars harmonic keyword

outputEnergies parameter

Biasing and analysis methods

outputEnergy colvars colvar bias keyword

outputEnergy colvars colvar keyword

outputEnergy colvars harmonic keyword

outputEnergy colvars histogramRestraint keyword

outputEnergy colvars metadynamics 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

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 keyword

Periodic components.

PME parameter

PMEGridSizeX parameter

PMEGridSizeY parameter

PMEGridSizeZ parameter

PMEGridSpacing parameter

PMEInterpOrder 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 atom group keyword

psfSegID colvars alpha keyword

alpha: $\alpha$ -helix content

psfSegID colvars dihedralPC keyword

Python scripting interface and

python command

ramd accel parameter

ramd debugLevel parameter

ramd firstProtAtom parameter

ramd firstRamdAtom parameter

ramd forceOutFreq parameter

ramd lastProtAtom parameter

ramd lastRamdAtom parameter

ramd maxDist parameter

ramd mdStart parameter

ramd mdSteps parameter

ramd ramdSeed parameter

ramd ramdSteps parameter

ramd rMinMd 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

ref colvars distanceXY keyword

ref2 colvars distanceZ keyword

ref2 colvars distanceXY keyword

refHistogram colvars histogramRestraint keyword

refHistogramFile colvars histogramRestraint keyword

refPositions colvars atom group keyword

refPositions colvars rmsd keyword

refPositions colvars eigenvector keyword

refPositions colvars orientation keyword

refPositions colvars orientationAngle keyword

refPositions colvars orientationProj keyword

refPositions colvars spinAngle keyword

refPositions colvars tilt keyword

refPositionsCol colvars atom group keyword

refPositionsCol colvars rmsd keyword

refPositionsCol colvars eigenvector keyword

refPositionsCol colvars orientation keyword

refPositionsCol colvars orientationAngle keyword

refPositionsCol colvars orientationProj keyword

refPositionsCol colvars spinAngle keyword

refPositionsCol colvars tilt keyword

refPositionsColValue colvars atom group keyword

refPositionsColValue colvars rmsd keyword

refPositionsColValue colvars eigenvector keyword

refPositionsColValue colvars orientation keyword

refPositionsColValue colvars orientationAngle keyword

refPositionsColValue colvars orientationProj keyword

refPositionsColValue colvars spinAngle keyword

refPositionsColValue colvars tilt keyword

refPositionsFile colvars atom group keyword

refPositionsFile colvars rmsd keyword

refPositionsFile colvars eigenvector keyword

refPositionsFile colvars orientation keyword

refPositionsFile colvars orientationAngle keyword

refPositionsFile colvars orientationProj keyword

refPositionsFile colvars spinAngle keyword

refPositionsFile colvars tilt 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

residueRange colvars dihedralPC keyword

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

Configuration keywords shared by

scalable colvars any component keyword

scnb parameter

Colvars as scripted functions

scriptedColvarForces colvars global keyword

Scripted biases

scriptedFunction colvars colvar keyword

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

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

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

StrainRate parameter

structure parameter

subtractAppliedForce colvars colvar keyword

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

targetEquilSteps colvars harmonic keyword

targetForceConstant colvars harmonic keyword

targetForceExponent colvars harmonic keyword

Moving restraints: umbrella sampling

targetNumStages colvars harmonic keyword

targetNumSteps colvars harmonic keyword

Python scripting interface and

tcl.call() command

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

topology alias psfgen command

topology psfgen command

TOTAL2 energy

TOTAL3 energy

Improving Parallel Scaling

twoAwayX

twoAwayY

Improving Parallel Scaling

twoAwayZ

Improving Parallel Scaling

units used for output

updateBias colvars abf keyword

updateFrequency colvars alb keyword

Grid definition for multidimensional

upperBoundaries colvars histogramGrid keyword

upperBoundary colvars colvar keyword

upperBoundary colvars histogramRestraint keyword

upperWall colvars colvar keyword

upperWallConstant colvars colvar keyword

useConstantArea parameter

useConstantRatio parameter

useFlexibleCell parameter

useGrids colvars metadynamics keyword

Performance tuning

useGroupPressure parameter

useSettle parameter

vdwForceSwitching parameter

vdwGeometricSigma parameter

vector colvars eigenvector keyword

vectorCol colvars eigenvector keyword

vectorColValue colvars eigenvector keyword

vectorFile colvars eigenvector keyword

vectorFile colvars dihedralPC keyword

vectorNumber colvars dihedralPC keyword

velDCDfile parameter

velDCDfreq parameter

velocities parameter

Velocity quenching parameters

velocityQuenching parameter

waterModel parameter

Water Models

wellTempered colvars metadynamics keyword

Well-tempered metadynamics

width colvars colvar keyword

Grid definition for multidimensional

widths colvars histogramGrid keyword

wrapAll parameter

wrapAround colvars distanceZ, dihedral or spinAngle 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

XSTfile parameter

XSTfreq parameter