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Index

1-4scaling parameter
Non-bonded force field parameters
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
accelMDLastStep parameter
NAMD parameters
accelMDOutFreq parameter
NAMD parameters
accelMDTalpha parameter
NAMD parameters
accelMDTE parameter
NAMD parameters
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
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
alchOutFile parameter
Implementation of the free
alchOutFreq parameter
Implementation of the free
alchType parameter
Implementation of the free
alchVdwLambdaEnd parameter
Implementation of the free
alchVdwShiftCoeff parameter
Implementation of the free
alias psfgen command
List of Commands | List of Commands
alphaCutoff parameter
Configuration Parameters
amber parameter
AMBER force field parameters
ambercoor parameter
AMBER force field parameters
analysis colvars global keyword
Configuration syntax for the
angleRef colvars alpha keyword
alpha: $ \alpha$ -helix content
angleTol colvars alpha keyword
alpha: $ \alpha$ -helix content
applyBias colvars abf keyword
Parameters for ABF
atomNameResidueRange colvars atom group keyword
Selection keywords
atomNumbers colvars atom group keyword
Selection keywords
atomNumbersRange colvars atom group keyword
Selection keywords
atoms colvars cartesian keyword
cartesian: vector of atomic
atoms colvars rmsd keyword
rmsd: root mean square
Atoms moving too fast
Non-bonded interaction distance-testing
atomsCol colvars atom group keyword
Selection keywords
atomsColValue colvars atom group keyword
Selection keywords
atomsFile colvars atom group keyword
Selection keywords
auto psfgen command
List of Commands
axis colvars distanceZ, distanceXY keyword
distanceZ: projection of a
axis colvars inertiaZ keyword
inertiaZ: total moment of
axis colvars tilt, spinAngle keyword
spinAngle: angle of rotation
Bad global exclusion count
Non-bonded interaction distance-testing
BerendsenPressure parameter
Tcl scripting interface and | Berendsen pressure bath coupling
BerendsenPressureCompressibility parameter
Tcl scripting interface and | Berendsen pressure bath coupling
BerendsenPressureFreq parameter
Berendsen pressure bath coupling
BerendsenPressureRelaxationTime parameter
Tcl scripting interface and | Berendsen pressure bath coupling
BerendsenPressureTarget parameter
Tcl scripting interface and | Berendsen pressure bath coupling
biasTemperature colvars metadynamics keyword
Well-tempered metadynamics
binaryoutput parameter
Tcl scripting interface and | Output files
binaryrestart parameter
Output files
bincoordinates parameter
Input files
binvelocities parameter
Input files
BOUNDARY energy
Standard output
callback command
Tcl scripting interface and
cellBasisVector1 parameter
Periodic boundary conditions
cellBasisVector2 parameter
Periodic boundary conditions
cellBasisVector3 parameter
Periodic boundary conditions
cellOrigin parameter
Periodic boundary conditions
centerReference colvars atom group keyword
Moving frame of reference.
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 NAMD configuration file keyword
NAMD parameters
colvars colvars colvar bias keyword
Biasing and analysis methods
colvarsConfig colvars NAMD configuration file keyword
NAMD parameters
colvarsInput colvars NAMD configuration file keyword
NAMD parameters
colvarsRestartFrequency colvars global keyword
Configuration syntax for the
colvarsTrajAppend colvars global keyword
Configuration syntax for the
colvarsTrajFrequency colvars global keyword
Configuration syntax for the
COMmotion parameter
Initialization
componentCoeff colvars any component keyword
Linear and polynomial combinations
componentExp colvars any component keyword
Linear and polynomial combinations
consexp parameter
Harmonic restraint parameters
consForceConfig command
Tcl scripting interface and | Constant Forces
consForceFile parameter
Constant Forces
consForceScaling parameter
Tcl scripting interface and | Constant Forces
conskcol parameter
Harmonic restraint parameters
conskfile parameter
Harmonic restraint parameters
consref parameter
Harmonic restraint parameters
constantForce parameter
Tcl scripting interface and | Constant Forces
constraints parameter
Harmonic restraint parameters
constraintScaling parameter
Tcl scripting interface and | Harmonic restraint parameters
coord psfgen command
List of Commands
coordinates parameter
Input files
coordpdb psfgen command
List of Commands
coorfile command
Tcl scripting interface and
corrFunc colvars colvar keyword
Statistical analysis of collective
corrFuncLength colvars colvar keyword
Statistical analysis of collective
corrFuncNormalize colvars colvar keyword
Statistical analysis of collective
corrFuncOffset colvars colvar keyword
Statistical analysis of collective
corrFuncOutputFile colvars colvar keyword
Statistical analysis of collective
corrFuncStride colvars colvar keyword
Statistical analysis of collective
corrFuncType colvars colvar keyword
Statistical analysis of collective
corrFuncWithColvar colvars colvar keyword
Statistical analysis of collective
cosAngles parameter
MARTINI Residue-Based Coarse-Grain Forcefield
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
dcdFile command
Multiple-copy/replica-exchange scripting interface
DCDfile parameter
Tcl scripting interface and | Output files
DCDfreq parameter
Output files
DCDUnitCell parameter
Output files
delatom psfgen command
List of Commands
dielectric parameter
Non-bonded force field parameters
differenceVector colvars eigenvector keyword
eigenvector: projection of the
drude parameter
Drude force field parameters
drudeBondConst parameter
Drude force field parameters
drudeBondLen parameter
Drude force field parameters
drudeDamping parameter
Drude force field parameters
drudeNbTholeCut parameter
Drude force field parameters
drudeTemp parameter
Drude force field parameters
dummyAtom colvars atom group keyword
Selection keywords
dumpPartialFreeEnergyFile colvars metadynamics keyword
Multiple-replicas metadynamics
eField parameter
Tcl scripting interface and | External Electric Field
eFieldFreq parameter
Tcl scripting interface and
eFieldNormalized parameter
External Electric Field
eFieldOn parameter
External Electric Field
eFieldPhase parameter
Tcl scripting interface and
enableFitGradients colvars atom group keyword
Moving frame of reference.
enableForces colvars atom group keyword
Moving frame of reference.
error message
Atoms moving too fast
Non-bonded interaction distance-testing
Bad global exclusion count
Non-bonded interaction distance-testing
exclude parameter
Non-bonded force field parameters
ExcludeFromPressure parameter
Nosé-Hoover Langevin piston pressure
ExcludeFromPressureCol parameter
Nosé-Hoover Langevin piston pressure
ExcludeFromPressureFile parameter
Nosé-Hoover Langevin piston pressure
exit command
Tcl scripting interface and
expandBoundaries colvars colvar keyword
General options for a
expDenom colvars coordNum keyword
coordNum: coordination number between
expNumer colvars coordNum keyword
coordNum: coordination number between
exponent colvars distanceInv keyword
distanceInv: mean distance between
extCoordFilename parameter
External Program Forces
extendedFluctuation colvars colvar keyword
Extended Lagrangian.
extendedLagrangian colvars colvar keyword
Extended Lagrangian.
extendedLangevinDamping colvars colvar keyword
Extended Lagrangian.
extendedSystem parameter
Periodic boundary conditions
extendedTemp colvars colvar keyword
Extended Lagrangian.
extendedTimeConstant colvars colvar keyword
Extended Lagrangian.
extForceFilename parameter
External Program Forces
extForces parameter
External Program Forces
extForcesCommand parameter
External Program Forces
extraBonds parameter
Extra bond, angle, and
extraBondsFile parameter
Extra bond, angle, and
FFTWEstimate parameter
PME parameters
FFTWUseWisdom parameter
PME parameters
FFTWWisdomFile parameter
PME parameters
first psfgen command
List of Commands
firsttimestep parameter
Timestep parameters
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
forceDCDfile parameter
Output files
forceDCDfreq parameter
Output files
forceNoPBC colvars distance keyword
distance: center-of-mass distance between
forceNoPBC colvars distanceZ, distanceXY keyword
distanceZ: projection of a
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
GBIS parameter
Configuration Parameters
GBISBeta parameter
Configuration Parameters
GBISDelta parameter
Configuration Parameters
GBISGamma parameter
Configuration Parameters
GoCoordinates parameter
Configuration file modifications
GoForcesOn parameter
Configuration file modifications
GoMethod parameter
Configuration file modifications
GoParameters parameter
Configuration file modifications
GPRESSAVG
Standard output
GPRESSURE
Standard output
grocoorfile parameter
GROMACS force field parameters | Configuration file modifications
gromacs parameter
GROMACS force field parameters | Configuration file modifications
GromacsPair parameter
Configuration file modifications
grotopfile parameter
GROMACS force field parameters | Configuration file modifications
group1 colvars distance keyword
distance: center-of-mass distance between
group2 colvars distance keyword
distance: center-of-mass distance between
group2CenterOnly colvars coordNum keyword
coordNum: coordination number between
guesscoord psfgen command
List of Commands
hardLowerBoundary colvars colvar keyword
General options for a
hardUpperBoundary colvars colvar keyword
General options for a
hBondCoeff colvars alpha keyword
alpha: $ \alpha$ -helix content
hBondCutoff colvars alpha keyword
alpha: $ \alpha$ -helix content
hBondExpDenom colvars alpha keyword
alpha: $ \alpha$ -helix content
hBondExpNumer colvars alpha keyword
alpha: $ \alpha$ -helix content
hgroupCutoff (Å) parameter
Non-bonded interaction distance-testing
hideJacobian colvars abf keyword
Parameters for ABF
hillWeight colvars metadynamics keyword
Metadynamics
hillWidth colvars metadynamics keyword
Performance tuning
historyFreq colvars abf keyword
Parameters for ABF
IMDfreq parameter
Interactive Molecular Dynamics (IMD)
IMDignore parameter
Interactive Molecular Dynamics (IMD)
IMDon parameter
Interactive Molecular Dynamics (IMD)
IMDport parameter
Interactive Molecular Dynamics (IMD)
IMDwait parameter
Interactive Molecular Dynamics (IMD)
indexFile colvars global keyword
Configuration syntax for the
indexGroup colvars atom group keyword
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
keepHills colvars metadynamics keyword
Compatibility and post-processing
lambdaSchedule colvars harmonic keyword
Changing force constant
langevin parameter
Langevin dynamics parameters
langevinCol parameter
Langevin dynamics parameters
langevinDamping parameter
Langevin dynamics parameters
langevinFile parameter
Langevin dynamics parameters
langevinHydrogen parameter
Langevin dynamics parameters
LangevinPiston parameter
Tcl scripting interface and | Nosé-Hoover Langevin piston pressure
LangevinPistonDecay parameter
Tcl scripting interface and | Nosé-Hoover Langevin piston pressure
LangevinPistonPeriod parameter
Tcl scripting interface and | Nosé-Hoover Langevin piston pressure
LangevinPistonTarget parameter
Tcl scripting interface and | Nosé-Hoover Langevin piston pressure
LangevinPistonTemp parameter
Tcl scripting interface and | Nosé-Hoover Langevin piston pressure
langevinTemp parameter
Tcl scripting interface and | Langevin dynamics parameters
last psfgen command
List of Commands
les parameter
Simulation
lesCol parameter
Simulation
lesFactor parameter
Simulation
lesFile parameter
Simulation
lesReduceMass parameter
Simulation
lesReduceTemp parameter
Simulation
limitdist parameter
Non-bonded force field parameters
LJcorrection parameter
Non-bonded force field parameters
longSplitting parameter
Multiple timestep parameters
loweAndersen parameter
Lowe-Andersen dynamics parameters
loweAndersenCutoff parameter
Lowe-Andersen dynamics parameters
loweAndersenRate parameter
Lowe-Andersen dynamics parameters
loweAndersenTemp parameter
Lowe-Andersen dynamics parameters
lowerBoundary colvars colvar keyword
General options for a
lowerWall colvars colvar keyword
Artificial boundary potentials (walls)
lowerWallConstant colvars colvar keyword
Artificial boundary potentials (walls)
main colvars distanceZ, distanceXY keyword
distanceZ: projection of a
margin parameter
Non-bonded interaction distance-testing
margin violations
Non-bonded interaction distance-testing
martiniDielAllow parameter
MARTINI Residue-Based Coarse-Grain Forcefield
martiniSwitching parameter
MARTINI Residue-Based Coarse-Grain Forcefield
maxForce colvars abf keyword
Parameters for ABF
maximumMove parameter
Velocity quenching parameters
measure command
Tcl scripting interface and
mergeCrossterms parameter
Standard output
mgridforce parameter
Grid Forces
mgridforcechargecol parameter
Grid Forces
mgridforcecol parameter
Grid Forces
mgridforcecont1 parameter
Grid Forces
mgridforcecont2 parameter
Grid Forces
mgridforcecont3 parameter
Grid Forces
mgridforcefile parameter
Grid Forces
mgridforcelite parameter
Grid Forces
mgridforcepotfile parameter
Grid Forces
mgridforcescale parameter
Grid Forces
mgridforcevoff parameter
Grid Forces
mgridforcevolts parameter
Grid Forces
minBabyStep parameter
Conjugate gradient parameters
minimization parameter
Conjugate gradient parameters
minimize command
Tcl scripting interface and
minLineGoal parameter
Conjugate gradient parameters
minTinyStep parameter
Conjugate gradient parameters
MISC energy
Standard output
molly parameter
Multiple timestep parameters
mollyIterations parameter
Multiple timestep parameters
mollyTolerance parameter
Multiple timestep parameters
movingConstraints parameter
Moving Constraints
movingConsVel parameter
Moving Constraints
MSM parameter
MSM parameters
MSMApprox parameter
MSM parameters
MSMBlockSizeX, MSMBlockSizeY, MSMBlockSizeZ parameter
MSM parameters
MSMGridSpacing parameter
MSM parameters
MSMLevels parameter
MSM parameters
MSMPadding parameter
MSM parameters
MSMQuality parameter
MSM parameters
MSMSerial parameter
MSM parameters
MSMSplit parameter
MSM parameters
MSMxmax, MSMymax, MSMzmax parameter
MSM parameters
MSMxmin, MSMymin, MSMzmin parameter
MSM parameters
MTSAlgorithm parameter
Multiple timestep parameters
multipleReplicas colvars metadynamics keyword
Multiple-replicas metadynamics
multiply psfgen command
List of Commands
mutate psfgen command
List of Commands
myReplica command
Multiple-copy/replica-exchange scripting interface
name colvars metadynamics keyword
Compatibility and post-processing
name colvars colvar keyword
General options for a
name colvars colvar bias keyword
Biasing and analysis methods
newHillFrequency colvars metadynamics keyword
Metadynamics
nonbondedFreq parameter
Multiple timestep parameters
nonbondedScaling parameter
Tcl scripting interface and | Non-bonded force field parameters
numNodes command
Tcl scripting interface and
numPes command
Tcl scripting interface and
numPhysicalNodes command
Tcl scripting interface and
numReplicas command
Multiple-copy/replica-exchange scripting interface
numsteps parameter
Timestep parameters
oneSiteSystemForce colvars distance keyword
distance: center-of-mass distance between
oneSiteSystemForce colvars distanceZ, distanceXY keyword
distanceZ: projection of a
oneSiteSystemForce colvars angle, dihedral keyword
dihedral: torsional angle 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
Moving restraints: steered molecular
outputAppliedForce colvars colvar keyword
Trajectory output
outputCenters colvars harmonic keyword
Moving restraints: steered molecular
outputEnergies parameter
Standard output
outputEnergy colvars colvar keyword
Trajectory output
outputEnergy colvars colvar bias keyword
Biasing and analysis methods
outputFreq colvars abf keyword
Parameters for ABF
outputFreq colvars histogram keyword
Multidimensional histograms
outputMomenta parameter
Standard output
outputname parameter
Output files
outputPairlists parameter
Non-bonded interaction distance-testing
outputPressure parameter
Standard output
outputSystemForce colvars colvar keyword
Trajectory output
outputTiming parameter
Standard 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
pairlistGrow parameter
Non-bonded interaction distance-testing
pairlistMinProcs parameter
Non-bonded interaction distance-testing
pairlistShrink parameter
Non-bonded interaction distance-testing
pairlistsPerCycle parameter
Non-bonded interaction distance-testing
pairlistTrigger parameter
Non-bonded interaction distance-testing
parameters parameter
Input files
paraTypeCharmm parameter
Input files
paraTypeXplor parameter
Input files
parmfile parameter
AMBER force field parameters
patch psfgen command
List of Commands
pdb psfgen command
List of Commands
pdbalias atom psfgen command
List of Commands
pdbalias residue psfgen command
List of Commands
period colvars distanceZ keyword
Periodic components.
PME parameter
PME parameters
PMEGridSizeX parameter
PME parameters
PMEGridSizeY parameter
PME parameters
PMEGridSizeZ parameter
PME parameters
PMEGridSpacing parameter
PME parameters
PMEInterpOrder parameter
PME parameters
PMEProcessors parameter
PME parameters
PMETolerance parameter
PME parameters
PRESSAVG
Standard output
pressureProfile parameter
Pressure profile calculations
pressureProfileAtomTypes parameter
Pressure profile calculations
pressureProfileAtomTypesCol parameter
Pressure profile calculations
pressureProfileAtomTypesFile parameter
Pressure profile calculations
pressureProfileEwald parameter
Pressure profile calculations
pressureProfileEwaldX parameter
Pressure profile calculations
pressureProfileEwaldY parameter
Pressure profile calculations
pressureProfileEwaldZ parameter
Pressure profile calculations
pressureProfileFreq parameter
Pressure profile calculations
pressureProfileSlabs parameter
Pressure profile calculations
print command
Tcl scripting interface and
psfcontext allcaps psfgen command
List of Commands
psfcontext create psfgen command
List of Commands
psfcontext delete psfgen command
List of Commands
psfcontext eval psfgen command
List of Commands
psfcontext mixedcase psfgen command
List of Commands
psfcontext psfgen command
List of Commands
psfcontext reset psfgen command
List of Commands
psfcontext stats psfgen command
List of Commands
psfSegID colvars atom group keyword
Selection keywords
psfSegID colvars alpha keyword
alpha: $ \alpha$ -helix content
ramd accel parameter
Random acceleration molecular dynamics
ramd debugLevel parameter
Random acceleration molecular dynamics
ramd firstProtAtom parameter
Random acceleration molecular dynamics
ramd firstRamdAtom parameter
Random acceleration molecular dynamics
ramd forceOutFreq parameter
Random acceleration molecular dynamics
ramd lastProtAtom parameter
Random acceleration molecular dynamics
ramd lastRamdAtom parameter
Random acceleration molecular dynamics
ramd maxDist parameter
Random acceleration molecular dynamics
ramd mdStart parameter
Random acceleration molecular dynamics
ramd mdSteps parameter
Random acceleration molecular dynamics
ramd ramdSeed parameter
Random acceleration molecular dynamics
ramd ramdSteps parameter
Random acceleration molecular dynamics
ramd rMinMd parameter
Random acceleration molecular dynamics
ramd rMinRamd parameter
Random acceleration molecular dynamics
rateMax colvars alb keyword
Adaptive Linear Bias/Experiment Directed
readexclusions parameter
AMBER force field parameters
readpsf psfgen command
List of Commands
reassignFreq parameter
Temperature reassignment parameters
reassignHold parameter
Temperature reassignment parameters
reassignIncr parameter
Temperature reassignment parameters
reassignTemp parameter
Tcl scripting interface and | Temperature reassignment parameters
rebinGrids colvars metadynamics keyword
Performance tuning
ref colvars distanceZ, distanceXY keyword
distanceZ: projection of a
ref2 colvars distanceZ, distanceXY keyword
distanceZ: projection of a
refPositions colvars atom group keyword
Moving frame of reference.
refPositions colvars rmsd keyword
rmsd: root mean square
refPositionsCol colvars atom group keyword
Moving frame of reference.
refPositionsCol colvars rmsd keyword
rmsd: root mean square
refPositionsColValue colvars atom group keyword
Moving frame of reference.
refPositionsColValue colvars rmsd keyword
rmsd: root mean square
refPositionsFile colvars atom group keyword
Moving frame of reference.
refPositionsFile colvars rmsd keyword
rmsd: root mean square
refPositionsGroup colvars atom group keyword
Moving frame of reference.
regenerate psfgen command
List of Commands | List of Commands
reinitatoms command
Tcl scripting interface and
reinitvels command
Tcl scripting interface and
reloadCharges command
Tcl scripting interface and
replica exchange
Replica exchange simulations
replicaAtomRecv command
Multiple-copy/replica-exchange scripting interface
replicaAtomSend command
Multiple-copy/replica-exchange scripting interface
replicaAtomSendrecv command
Multiple-copy/replica-exchange scripting interface
replicaBarrier command
Multiple-copy/replica-exchange scripting interface
replicaDcdFile command
Multiple-copy/replica-exchange scripting interface
replicaEval command
Multiple-copy/replica-exchange scripting interface
replicaID colvars metadynamics keyword
Multiple-replicas metadynamics
replicaRecv command
Multiple-copy/replica-exchange scripting interface
replicaSend command
Multiple-copy/replica-exchange scripting interface
replicaSendrecv command
Multiple-copy/replica-exchange scripting interface
replicasRegistry colvars metadynamics keyword
Multiple-replicas metadynamics
replicaUniformPatchGrids parameter
Multiple-copy/replica-exchange scripting interface
replicaUpdateFrequency colvars metadynamics keyword
Multiple-replicas metadynamics
replicaYield command
Multiple-copy/replica-exchange scripting interface
rescaleFreq parameter
Temperature rescaling parameters
rescaleTemp parameter
Tcl scripting interface and | Temperature rescaling parameters
rescalevels command
Tcl scripting interface and
resetpsf psfgen command
List of Commands
residue psfgen command
List of Commands
residueRange colvars alpha keyword
alpha: $ \alpha$ -helix content
restartfreq parameter
Output files
restartname parameter
Tcl scripting interface and | Output files
restartsave parameter
Output files
rigidBonds parameter
Bond constraint parameters
rigidDieOnError parameter
Bond constraint parameters
rigidIterations parameter
Bond constraint parameters
rigidTolerance parameter
Bond constraint parameters
rotateReference colvars atom group keyword
Moving frame of reference.
rotConsAxis parameter
Rotating Constraints
rotConsPivot parameter
Rotating Constraints
rotConstraints parameter
Rotating Constraints
rotConsVel parameter
Rotating Constraints
run command
Tcl scripting interface and
run norepeat command
Tcl scripting interface and
runAve colvars colvar keyword
Statistical analysis of collective
runAveLength colvars colvar keyword
Statistical analysis of collective
runAveOutputFile colvars colvar keyword
Statistical analysis of collective
runAveStride colvars colvar keyword
Statistical analysis of collective
SASA parameter
Configuration Parameters
saveFreeEnergyFile colvars metadynamics keyword
Output files
scnb parameter
AMBER force field parameters
scriptedColvarForces colvars global keyword
Scripted biases
scriptedFunction colvars colvar keyword
Colvars as scripted functions
scriptedFunctionType colvars colvar keyword
Colvars as scripted functions
scriptedFunctionVectorSize colvars colvar keyword
Colvars as scripted functions
seed parameter
Initialization
segment psfgen command
List of Commands
selectConstraints parameter
Harmonic restraint parameters
selectConstrX parameter
Harmonic restraint parameters
selectConstrY parameter
Harmonic restraint parameters
selectConstrZ parameter
Harmonic restraint parameters
shared colvars abf keyword
Multiple-replica ABF
sharedFreq colvars abf keyword
Multiple-replica ABF
SMD parameter
Parameters
SMDDir parameter
Parameters
SMDFile parameter
Parameters
SMDk parameter
Parameters
SMDk2 parameter
Parameters
SMDOutputFreq parameter
Parameters
SMDVel parameter
Parameters
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
StrainRate parameter
Nosé-Hoover Langevin piston pressure
structure parameter
Input files
surfaceTension parameter
Configuration Parameters
SurfaceTensionTarget parameter
Tcl scripting interface and | Nosé-Hoover Langevin piston pressure
switchdist parameter
Non-bonded force field parameters
switching parameter
Non-bonded force field parameters
symmetryFile parameter
Symmetry Restraints
symmetryFirstFullStep parameter
Symmetry Restraints
symmetryFirstStep parameter
Symmetry Restraints
symmetryk parameter
Symmetry Restraints
symmetrykFile parameter
Symmetry Restraints
symmetryLastFullStep parameter
Symmetry Restraints
symmetryLastStep parameter
Symmetry Restraints
symmetryMatrixFile parameter
Symmetry Restraints
symmetryRestraints parameter
Symmetry Restraints
symmetryScaleForces parameter
Symmetry Restraints
tableInterpType parameter
Tabulated nonbonded interaction parameters
tabulatedEnergies parameter
Tabulated nonbonded interaction parameters
tabulatedEnergiesFile parameter
Tabulated nonbonded interaction parameters
targetCenters colvars harmonic keyword
Moving restraints: steered molecular
targetEquilSteps colvars harmonic keyword
Changing force constant
targetForceConstant colvars harmonic keyword
Changing force constant
targetForceExponent colvars harmonic keyword
Changing force constant
targetNumStages colvars harmonic keyword
Moving restraints: umbrella sampling
targetNumSteps colvars harmonic keyword
Moving restraints: steered molecular
tclBC parameter
Tcl Boundary Forces
tclBCArgs parameter
Tcl Boundary Forces
tclBCScript parameter
Tcl Boundary Forces
tclForces parameter
Tcl Forces and Analysis
tclForcesScript parameter
Tcl Forces and Analysis
tCouple parameter
Temperature coupling parameters
tCoupleCol parameter
Temperature coupling parameters
tCoupleFile parameter
Temperature coupling parameters
tCoupleTemp parameter
Temperature coupling parameters
TEMPAVG
Standard output
temperature parameter
Initialization
timestep parameter
Timestep parameters
TMD parameter
Targeted Molecular Dynamics (TMD)
TMDDiffRMSD parameter
Targeted Molecular Dynamics (TMD)
TMDFile parameter
Targeted Molecular Dynamics (TMD)
TMDFile2 parameter
Targeted Molecular Dynamics (TMD)
TMDFinalRMSD parameter
Targeted Molecular Dynamics (TMD)
TMDFirstStep parameter
Targeted Molecular Dynamics (TMD)
TMDInitialRMSD parameter
Targeted Molecular Dynamics (TMD)
TMDk parameter
Targeted Molecular Dynamics (TMD)
TMDLastStep parameter
Targeted Molecular Dynamics (TMD)
TMDOutputFreq parameter
Targeted Molecular Dynamics (TMD)
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
units used for output
PDB files | DCD trajectory files | DCD trajectory files | NAMD binary files | Output files | Standard output
updateBias colvars abf keyword
Parameters for ABF
updateFrequency colvars alb keyword
Adaptive Linear Bias/Experiment Directed
upperBoundary colvars colvar keyword
General options for a
upperWall colvars colvar keyword
Artificial boundary potentials (walls)
upperWallConstant colvars colvar keyword
Artificial boundary potentials (walls)
useConstantArea parameter
Tcl scripting interface and | Pressure Control
useConstantRatio parameter
Tcl scripting interface and | Pressure Control
useFlexibleCell parameter
Tcl scripting interface and | Pressure Control
useGrids colvars metadynamics keyword
Performance tuning
useGroupPressure parameter
Tcl scripting interface and | Pressure Control
useSettle parameter
Bond constraint parameters
vdwForceSwitching parameter
Non-bonded force field parameters
vdwGeometricSigma parameter
Non-bonded force field parameters
vector colvars eigenvector keyword
eigenvector: projection of the
vectorCol colvars eigenvector keyword
eigenvector: projection of the
vectorColValue colvars eigenvector keyword
eigenvector: projection of the
vectorFile colvars eigenvector keyword
eigenvector: projection of the
vectorFile colvars dihedralPC keyword
dihedralPC: protein dihedral pricipal
vectorNumber colvars dihedralPC keyword
dihedralPC: protein dihedral pricipal
velDCDfile parameter
Output files
velDCDfreq parameter
Output files
velocities parameter
Input files
velocityQuenching parameter
Velocity quenching parameters
waterModel parameter
Water Models
wellTempered colvars metadynamics keyword
Well-tempered metadynamics
width colvars colvar keyword
General options for a
wrapAll parameter
Periodic boundary conditions
wrapAround colvars distanceZ, dihedral or spinAngle keyword
Periodic components.
wrapNearest parameter
Periodic boundary conditions
wrapWater parameter
Periodic boundary conditions
writeFreeEnergyFile colvars metadynamics keyword
Output files
writeHillsTrajectory colvars metadynamics keyword
Compatibility and post-processing
writenamdbin psfgen command
List of Commands
writepdb psfgen command
List of Commands
writepsf psfgen command
List of Commands
XSTfile parameter
Periodic boundary conditions
XSTfreq parameter
Periodic boundary conditions
zeroMomentum parameter
Conserving momentum



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