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Index

1-4scaling parameter
Non-bonded force field parameters
cphRun command
New Commands and Keywords
cphRun command
New Commands and Keywords
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
abf
colvars
Parameters for ABF
name
Parameters for ABF
outputEnergy
Parameters for ABF
outputFreq
Parameters for ABF
stepZeroData
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 principal
residueRange
dihedralPC: protein dihedral principal
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
dipoleMagnitude
atoms
dipoleMagnitude: dipole magnitude of
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
stepZeroData
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
stepZeroData
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
bypassExtendedLagrangian
Multidimensional histograms
colvars
Multidimensional histograms
name
Multidimensional histograms
outputFreq
Multidimensional histograms
stepZeroData
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 configuration keywords
name
Basic configuration keywords
outputEnergy
Basic configuration keywords
outputFreq
Basic configuration keywords
stepZeroData
Basic configuration keywords
writeTIPMF
Basic configuration keywords
writeTISamples
Basic configuration keywords
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
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
accelMDGStatWindow 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
alchRepLambdaEnd parameter
Implementation of the free
alchType parameter
Implementation of the free
alchVdwLambdaEnd parameter
Implementation of the free
alchVdwShiftCoeff parameter
Implementation of the free
alchWCA parameter
Implementation of the free
alias psfgen command
List of Commands | List of Commands
alphaCutoff parameter
Configuration Parameters
amber parameter
AMBER file and force
ambercoor parameter
AMBER file and force
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
atomPermutation colvars rmsd keyword
rmsd: root mean square
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 colvars cartesian keyword
cartesian: vector of atomic
atoms colvars gspath and gzpath keyword
gspath: progress along a
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
bondedCUDA parameter
Keywords
BOUNDARY energy
Standard output
bypassExtendedLagrangian colvars colvar bias keyword
Biasing and analysis methods
bypassExtendedLagrangian colvars harmonicWalls keyword
Harmonic wall restraints
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
drudeHardWall 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
ebMeta colvars metadynamics keyword
Ensemble-Biased Metadynamics
ebMetaEquilSteps colvars metadynamics keyword
Ensemble-Biased 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
extraBondsCosAngles 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
fittingAtoms colvars gspath and gspath keyword
gspath: progress along a
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
gaussianSigmas colvars metadynamics keyword
Basic configuration keywords
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 file support | Configuration file modifications
gromacs parameter
GROMACS file support | Configuration file modifications
GromacsPair parameter
Configuration file modifications
grotopfile parameter
GROMACS file support | 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
Basic configuration keywords
hillWidth colvars metadynamics keyword
Basic configuration keywords
historyFreq colvars abf keyword
Parameters for ABF
hmassrepart psfgen command
New Commands in the
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
Performance optimization
lambda colvars aspathCV and azpathCV keyword
aspathCV: progress along a
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
mapName colvars mapTotal keyword
mapTotal: total value of
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-walker metadynamics
multiply psfgen command
List of Commands
mutate psfgen command
List of Commands
myReplica command
Multiple-copy/replica-exchange scripting interface
name colvars atom group keyword
Selecting atoms
name colvars colvar bias keyword
Biasing and analysis methods
name colvars colvar keyword
Defining collective variables
name colvars any component keyword
Shared keywords for all
newHillFrequency colvars metadynamics keyword
Basic configuration keywords
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 colvar bias keyword
Biasing and analysis methods
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 file and force
patch psfgen command
List of Commands
pathFile colvars gspathCV and gzpathCV keyword
gspathCV: progress along a
pathFile colvars aspathCV and azpathCV keyword
aspathCV: progress along a
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
PMEoffload parameter
Keywords
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
psfgen_logfile psfgen command
New Commands in the
psfSegID colvars atom group keyword
Atom selection keywords
psfSegID colvars alpha keyword
alpha: $ \alpha$ -helix content
psfset psfgen command
List of Commands
python command
Python scripting interface and
qmBaseDir parameter
Keywords
qmBondColumn parameter
Keywords
qmBondDist parameter
Keywords
qmBondScheme parameter
Keywords
qmBondValueType parameter
Keywords
qmCharge parameter
Keywords
qmChargeFromPSF parameter
Keywords
qmChargeMode parameter
Keywords
qmColumn parameter
Keywords
qmConfigLine parameter
Keywords
qmCSMD parameter
Keywords
qmCSMDFile parameter
Keywords
qmCustomPCFile parameter
Keywords
qmCustomPCSelection parameter
Keywords
qmElecEmbed parameter
Keywords
qmEnergyStride parameter
Keywords
qmExecPath parameter
Keywords
qmForces parameter
Keywords
qmLinkElement parameter
Keywords
qmLiveSolventSel parameter
Keywords
qmLSSFreq parameter
Keywords
qmLSSMode parameter
Keywords
qmLSSRef parameter
Keywords
qmLSSResname parameter
Keywords
qmMult parameter
Keywords
qmOutStride parameter
Keywords
qmParamPDB parameter
Keywords
qmPCStride parameter
Keywords
qmPointChargeScheme parameter
Keywords
qmPositionOutStride parameter
Keywords
qmPrepProc parameter
Keywords
qmReplaceAll parameter
Keywords
qmSecProc parameter
Keywords
qmSimsPerNode parameter
Keywords
qmSoftware parameter
Keywords
qmSwitching parameter
Keywords
qmSwitchingType parameter
Keywords
qmVdwParams parameter
Keywords
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 file and force
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 optimization
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
refPositionsCol colvars gspath and gzpath keyword
gspath: progress along a
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
refPositionsFileN colvars gspath and gzpath keyword
gspath: progress along a
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-walker 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-walker metadynamics
replicaUniformPatchGrids parameter
Multiple-copy/replica-exchange scripting interface
replicaUpdateFrequency colvars metadynamics keyword
Multiple-walker 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 file and force
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
sdBondScaling parameter
Hybrid single-dual topology approach
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
singleTopology parameter
Hybrid single-dual topology approach
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
stepZeroData colvars colvar bias keyword
Biasing and analysis methods
stochRescale parameter
Stochastic velocity rescaling parameters
stochRescaleFreq parameter
Stochastic velocity rescaling parameters
stochRescaleHeat 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
targetDistFile colvars metadynamics keyword
Ensemble-Biased Metadynamics
targetDistMinVal colvars metadynamics keyword
Ensemble-Biased Metadynamics
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
timeStepFactor colvars colvar keyword
Multiple time-step variables
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 colvars global keyword
Units in the Colvars
units used for output
PDB files | DCD trajectory files | DCD trajectory files | NAMD binary files | Output files | Standard output
unperturbedBondFile parameter
Hybrid single-dual topology approach
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 optimization
useGroupPressure parameter
Tcl scripting interface and | Pressure Control
usePMECUDA parameter
Keywords
useSecondClosestFrame colvars gspath and gzpath keyword
gspath: progress along a
useSecondClosestFrame colvars gspathCV and gzpathCV keyword
gspathCV: progress along a
useSettle parameter
Bond constraint parameters
useThirdClosestFrame colvars gspath and gzpath keyword
gspath: progress along a
useThirdClosestFrame colvars gspathCV and gzpathCV keyword
gspathCV: progress along a
useZsquare colvars gzpath keyword
gzpath: distance from a
useZsquare colvars gzpathCV keyword
gzpathCV: distance from a
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 principal
vectorNumber colvars dihedralPC keyword
dihedralPC: protein dihedral principal
velDCDfile parameter
Output files
velDCDfreq parameter
Output files
velocities parameter
Input files
velocityQuenching parameter
Velocity quenching parameters
vpbonds psfgen command
New Commands in the
waterModel parameter
Water Models
weights colvars aspathCV and azpathCV keyword
aspathCV: progress along a
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
Output files
writeHistogram colvars metadynamics keyword
Probability distribution-restraints
writenamdbin psfgen command
List of Commands
writePartialFreeEnergyFile colvars metadynamics keyword
Multiple-walker metadynamics
writepdb psfgen command
List of Commands
writepsf psfgen command
List of Commands
writeTIPMF colvars colvar bias keyword
Thermodynamic integration
writeTISamples colvars colvar bias keyword
Thermodynamic integration
XSTfile parameter
Periodic boundary conditions
XSTfreq parameter
Periodic boundary conditions
zeroMomentum parameter
Conserving momentum



http://www.ks.uiuc.edu/Research/namd/