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Index

1-4scaling parameter
Non-bonded force field parameters
colvars parameter
NAMD parameters
colvarsConfig parameter
NAMD parameters
colvarsInput parameter
NAMD parameters
colvarsTrajFrequency parameter
Colvars module configuration file
colvarsTrajAppend parameter
Colvars module configuration file
colvarsRestartFrequency parameter
Colvars module configuration file
analysis parameter
Colvars module configuration file
name parameter
Colvar grid parameters
width parameter
Colvar grid parameters
lowerBoundary parameter
Colvar grid parameters
upperBoundary parameter
Colvar grid parameters
expandBoundaries parameter
Colvar grid parameters
lowerWall parameter
Boundary potentials (walls)
lowerWallConstant parameter
Boundary potentials (walls)
upperWall parameter
Boundary potentials (walls)
upperWallConstant parameter
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
period parameter
Periodic components.
wrapAround parameter
Periodic components.
group1 parameter
Component distance: center-of-mass distance
group2 parameter
Component distance: center-of-mass distance
forceNoPBC parameter
Component distance: center-of-mass distance
oneSiteSystemForce parameter
Component distance: center-of-mass distance
main parameter
Component distanceZ: projection of
ref parameter
Component distanceZ: projection of
ref2 parameter
Component distanceZ: projection of
axis parameter
Component distanceZ: projection of
forceNoPBC parameter
Component distanceZ: projection of
oneSiteSystemForce parameter
Component distanceZ: projection of
oneSiteSystemForce parameter
Component dihedral: torsional angle
cutoff parameter
Component coordNum: coordination number
expNumer parameter
Component coordNum: coordination number
expDenom parameter
Component coordNum: coordination number
cutoff3 parameter
Component coordNum: coordination number
group2CenterOnly parameter
Component coordNum: coordination number
atoms parameter
Component rmsd: root mean
refPositions parameter
Component rmsd: root mean
refPositionsFile parameter
Component rmsd: root mean
refPositionsCol parameter
Component rmsd: root mean
refPositionsColValue parameter
Component rmsd: root mean
vector parameter
Component eigenvector: projection of
vectorFile parameter
Component eigenvector: projection of
vectorCol parameter
Component eigenvector: projection of
vectorColValue parameter
Component eigenvector: projection of
closestToQuaternion parameter
Component orientation: orientation from
residueRange parameter
Component alpha: $ \alpha $-helix content
psfSegID parameter
Component alpha: $ \alpha $-helix content
hBondCoeff parameter
Component alpha: $ \alpha $-helix content
angleRef parameter
Component alpha: $ \alpha $-helix content
angleTol parameter
Component alpha: $ \alpha $-helix content
hBondCutoff parameter
Component alpha: $ \alpha $-helix content
hBondExpNumer parameter
Component alpha: $ \alpha $-helix content
hBondExpDenom parameter
Component alpha: $ \alpha $-helix content
vectorFile parameter
Component dihedralPC: protein dihedral
vectorNumber parameter
Component dihedralPC: protein dihedral
componentCoeff parameter
Linear and polynomial combinations
componentExp parameter
Linear and polynomial combinations
atomNumbers parameter
Defining atom groups
atomNumbersRange parameter
Defining atom groups
atomNameResidueRange parameter
Defining atom groups
psfSegID parameter
Defining atom groups
atomsFile parameter
Defining atom groups
atomsCol parameter
Defining atom groups
atomsColValue parameter
Defining atom groups
dummyAtom parameter
Defining atom groups
centerReference parameter
Defining atom groups
rotateReference parameter
Defining atom groups
refPositions parameter
Defining atom groups
refPositionsFile parameter
Defining atom groups
refPositionsCol parameter
Defining atom groups
refPositionsColValue parameter
Defining atom groups
refPositionsGroup parameter
Defining atom groups
disableForces parameter
Defining atom groups
corrFunc parameter
Statistical analysis of individual
corrFuncWithColvar parameter
Statistical analysis of individual
corrFuncType parameter
Statistical analysis of individual
corrFuncNormalize parameter
Statistical analysis of individual
corrFuncLength parameter
Statistical analysis of individual
corrFuncStride parameter
Statistical analysis of individual
corrFuncOffset parameter
Statistical analysis of individual
corrFuncOutputFile parameter
Statistical analysis of individual
runAve parameter
Statistical analysis of individual
runAveLength parameter
Statistical analysis of individual
runAveStride parameter
Statistical analysis of individual
runAveOutputFile parameter
Statistical analysis of individual
name parameter
Biasing and analysis methods
colvars parameter
Biasing and analysis methods
hillWeight parameter
Metadynamics
newHillFrequency parameter
Metadynamics
wellTempered parameter
Metadynamics
biasTemperature parameter
Metadynamics
useGrids parameter
Metadynamics
hillWidth parameter
Metadynamics
dumpFreeEnergyFile parameter
Metadynamics
rebinGrids parameter
Metadynamics
multipleReplicas parameter
Metadynamics
replicaID parameter
Metadynamics
replicasRegistry parameter
Metadynamics
replicaUpdateFrequency parameter
Metadynamics
dumpPartialFreeEnergyFile parameter
Metadynamics
name parameter
Metadynamics
saveFreeEnergyFile parameter
Metadynamics
keepHills parameter
Metadynamics
writeHillsTrajectory parameter
Metadynamics
forceConstant parameter
Harmonic restraints and Steered
centers parameter
Harmonic restraints and Steered
targetCenters parameter
Harmonic restraints and Steered
targetForceConstant parameter
Harmonic restraints and Steered
targetForceExponent parameter
Harmonic restraints and Steered
targetNumSteps parameter
Harmonic restraints and Steered
targetEquilSteps parameter
Harmonic restraints and Steered
targetNumStages parameter
Harmonic restraints and Steered
lambdaSchedule parameter
Harmonic restraints and Steered
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
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
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
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
gromacs parameter
GROMACS force field parameters
grotopfile parameter
GROMACS force field parameters
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
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
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
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
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
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
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
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
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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