Index

1-4scaling parameter

Non-bonded force field parameters

name parameter

Biasing and analysis methods

colvars parameter

Biasing and analysis methods

outputEnergy parameter

Biasing and analysis methods

hillWeight parameter

Metadynamics

newHillFrequency parameter

Metadynamics

writeFreeEnergyFile parameter

Output files

saveFreeEnergyFile parameter

Output files

useGrids parameter

Performance tuning

hillWidth parameter

Performance tuning

rebinGrids parameter

Performance tuning

wellTempered parameter

Well-tempered metadynamics

biasTemperature parameter

Well-tempered metadynamics

multipleReplicas parameter

Multiple-replicas metadynamics

replicaID parameter

Multiple-replicas metadynamics

replicasRegistry parameter

Multiple-replicas metadynamics

replicaUpdateFrequency parameter

Multiple-replicas metadynamics

dumpPartialFreeEnergyFile parameter

Multiple-replicas metadynamics

name parameter

Compatibility and post-processing

keepHills parameter

Compatibility and post-processing

writeHillsTrajectory parameter

Compatibility and post-processing

forceConstant parameter

Harmonic restraints

centers parameter

Harmonic restraints

targetCenters parameter

Moving restraints: steered molecular

targetNumSteps parameter

Moving restraints: steered molecular

outputCenters parameter

Moving restraints: steered molecular

outputAccumulatedWork parameter

Moving restraints: steered molecular

targetNumStages parameter

Moving restraints: umbrella sampling

targetForceConstant parameter

Changing force constant

targetForceExponent parameter

Changing force constant

targetEquilSteps parameter

Changing force constant

lambdaSchedule parameter

Changing force constant

colvars parameter

NAMD parameters

colvarsConfig parameter

NAMD parameters

colvarsInput parameter

NAMD parameters

colvarsTrajFrequency parameter

Configuration file for the

colvarsTrajAppend parameter

Configuration file for the

colvarsRestartFrequency parameter

Configuration file for the

indexFile parameter

Configuration file for the

analysis parameter

Configuration file for the

name parameter

General options for a

width parameter

General options for a

lowerBoundary parameter

General options for a

upperBoundary parameter

General options for a

hardLowerBoundary parameter

General options for a

hardUpperBoundary parameter

General options for a

expandBoundaries parameter

General options for a

lowerWallConstant parameter

Artificial boundary potentials (walls)

lowerWall parameter

Artificial boundary potentials (walls)

upperWallConstant parameter

Artificial boundary potentials (walls)

upperWall parameter

Artificial boundary potentials (walls)

outputValue parameter

Trajectory output

outputVelocity parameter

Trajectory output

outputEnergy parameter

Trajectory output

outputSystemForce parameter

Trajectory output

outputAppliedForce parameter

Trajectory output

extendedLagrangian parameter

Extended Lagrangian.

extendedFluctuation parameter

Extended Lagrangian.

extendedTimeConstant parameter

Extended Lagrangian.

extendedTemp parameter

Extended Lagrangian.

extendedLangevinDamping parameter

Extended Lagrangian.

corrFunc parameter

Statistical analysis of collective

corrFuncWithColvar parameter

Statistical analysis of collective

corrFuncType parameter

Statistical analysis of collective

corrFuncNormalize parameter

Statistical analysis of collective

corrFuncLength parameter

Statistical analysis of collective

corrFuncStride parameter

Statistical analysis of collective

corrFuncOffset parameter

Statistical analysis of collective

corrFuncOutputFile parameter

Statistical analysis of collective

runAve parameter

Statistical analysis of collective

runAveLength parameter

Statistical analysis of collective

runAveStride parameter

Statistical analysis of collective

runAveOutputFile parameter

Statistical analysis of collective

atomNumbers parameter

Selection keywords

indexGroup parameter

Selection keywords

atomNumbersRange parameter

Selection keywords

atomNameResidueRange parameter

Selection keywords

psfSegID parameter

Selection keywords

atomsFile parameter

Selection keywords

atomsCol parameter

Selection keywords

atomsColValue parameter

Selection keywords

dummyAtom parameter

Selection keywords

centerReference parameter

Moving frame of reference.

rotateReference parameter

Moving frame of reference.

refPositions parameter

Moving frame of reference.

refPositionsFile parameter

Moving frame of reference.

refPositionsCol parameter

Moving frame of reference.

refPositionsColValue parameter

Moving frame of reference.

refPositionsGroup parameter

Moving frame of reference.

enableFitGradients parameter

Moving frame of reference.

enableForces parameter

Moving frame of reference.

group1 parameter

distance: center-of-mass distance between

group2 parameter

distance: center-of-mass distance between

forceNoPBC parameter

distance: center-of-mass distance between

oneSiteSystemForce parameter

distance: center-of-mass distance between

main parameter

distanceZ: projection of a

ref parameter

distanceZ: projection of a

ref2 parameter

distanceZ: projection of a

axis parameter

distanceZ: projection of a

forceNoPBC parameter

distanceZ: projection of a

oneSiteSystemForce parameter

distanceZ: projection of a

exponent parameter

distanceInv: mean distance between

oneSiteSystemForce parameter

dihedral: torsional angle between

cutoff parameter

coordNum: coordination number between

cutoff3 parameter

coordNum: coordination number between

expNumer parameter

coordNum: coordination number between

expDenom parameter

coordNum: coordination number between

group2CenterOnly parameter

coordNum: coordination number between

atoms parameter

rmsd: root mean square

refPositions parameter

rmsd: root mean square

refPositionsFile parameter

rmsd: root mean square

refPositionsCol parameter

rmsd: root mean square

refPositionsColValue parameter

rmsd: root mean square

vector parameter

eigenvector: projection of the

vectorFile parameter

eigenvector: projection of the

vectorCol parameter

eigenvector: projection of the

vectorColValue parameter

eigenvector: projection of the

differenceVector parameter

eigenvector: projection of the

axis parameter

inertiaZ: total moment of

closestToQuaternion parameter

orientation: orientation from reference

axis parameter

spinAngle: angle of rotation

residueRange parameter

alpha: $\alpha$ -helix content

psfSegID parameter

alpha: $\alpha$ -helix content

hBondCoeff parameter

alpha: $\alpha$ -helix content

angleRef parameter

alpha: $\alpha$ -helix content

angleTol parameter

alpha: $\alpha$ -helix content

hBondCutoff parameter

alpha: $\alpha$ -helix content

hBondExpNumer parameter

alpha: $\alpha$ -helix content

hBondExpDenom parameter

alpha: $\alpha$ -helix content

vectorFile parameter

dihedralPC: protein dihedral pricipal

vectorNumber parameter

dihedralPC: protein dihedral pricipal

period parameter

Periodic components.

wrapAround parameter

Periodic components.

componentCoeff parameter

Linear and polynomial combinations

componentExp parameter

Linear and polynomial combinations

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

applyBias parameter

Parameters for ABF

Atoms moving too fast

Non-bonded interaction distance-testing

auto psfgen command

List of Commands

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

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

checkpoint command

Tcl scripting interface and

COMmotion parameter

Initialization

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

cosAngles parameter

MARTINI Residue-Based Coarse-Grain Forcefield

cutoff parameter

Non-bonded force field parameters

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 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

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

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

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

extCoordFilename parameter

External Program Forces

extendedSystem parameter

Periodic boundary conditions

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

forceDCDfile parameter

Output files

forceDCDfreq parameter

Output files

FullDirect parameter

Full direct parameters

fullElectFrequency parameter

Multiple timestep parameters

fullSamples parameter

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

guesscoord psfgen command

List of Commands

hgroupCutoff (Å) parameter

Non-bonded interaction distance-testing

hideJacobian parameter

Parameters for ABF

historyFreq parameter

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)

inputPrefix parameter

Parameters for ABF

intrinsicRadiusOffset parameter

Configuration Parameters

ionConcentration parameter

Configuration Parameters

isset command

Tcl scripting interface and

istrue command

Tcl scripting interface and

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

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 parameter

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

MTSAlgorithm parameter

Multiple timestep parameters

multiply psfgen command

List of Commands

mutate psfgen command

List of Commands

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

numsteps parameter

Timestep parameters

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

outputEnergies parameter

Standard output

outputFreq parameter

Parameters for ABF | Multidimensional histograms

outputMomenta parameter

Standard output

outputname parameter

Output files

outputPairlists parameter

Non-bonded interaction distance-testing

outputPressure parameter

Standard output

outputTiming parameter

Standard 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

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

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

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

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

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

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

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

SASA parameter

Configuration Parameters

scnb parameter

AMBER force field parameters

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

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

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

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 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 parameter

Parameters for ABF

useConstantArea parameter

Tcl scripting interface and | Pressure Control

useConstantRatio parameter

Tcl scripting interface and | Pressure Control

useFlexibleCell parameter

Tcl scripting interface and | Pressure Control

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

velDCDfile parameter

Output files

velDCDfreq parameter

Output files

velocities parameter

Input files

velocityQuenching parameter

Velocity quenching parameters

waterModel parameter

Water Models

wrapAll parameter

Periodic boundary conditions

wrapNearest parameter

Periodic boundary conditions

wrapWater parameter

Periodic boundary conditions

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