File List

Here is a list of all files with brief descriptions:

[detail level 123]

▶ adjmat
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ multicolvar
ActionVolume.h
AtomValuePack.h
BridgedMultiColvarFunction.h
CatomPack.h
MultiColvar.h
MultiColvarBase.h
MultiColvarFilter.h
MultiColvarFunction.h
VolumeGradientBase.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
ActionWithInputMatrix.cpp
ActionWithInputMatrix.h
AdjacencyMatrixBase.cpp
AdjacencyMatrixBase.h
AdjacencyMatrixVessel.cpp
AdjacencyMatrixVessel.h
AlignedMatrixBase.cpp
AlignedMatrixBase.h
ClusterAnalysisBase.cpp
ClusterAnalysisBase.h
ClusterDiameter.cpp
ClusterDistribution.cpp
ClusteringBase.cpp
ClusteringBase.h
ClusterProperties.cpp
ClusterSize.cpp
ClusterWithSurface.cpp
ContactAlignedMatrix.cpp
ContactMatrix.cpp
DFSClustering.cpp
HbondMatrix.cpp
MatrixColumnSums.cpp
MatrixRowSums.cpp
OutputCluster.cpp
SMACMatrix.cpp
Sprint.cpp
▶ analysis
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ gridtools
ActionWithGrid.h
ActionWithInputGrid.h
AverageOnGrid.h
ContourFindingBase.h
GridPrintingBase.h
GridVessel.h
HistogramOnGrid.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
MultiReferenceBase.h
PointWiseMapping.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
Analysis.cpp
Analysis.h
AnalysisWithLandmarks.cpp
AnalysisWithLandmarks.h
Average.cpp
AverageVessel.cpp
AverageVessel.h
ClassicalMultiDimensionalScaling.cpp
ClassicalScaling.cpp
ClassicalScaling.h
Commit.cpp
Histogram.cpp
LandmarkRegister.cpp
LandmarkRegister.h
LandmarkSelectionBase.cpp
LandmarkSelectionBase.h
PCA.cpp
SelectAllFrames.cpp
▶ bias
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ABMD.cpp
ActionRegister.h
Bias.cpp
Bias.h
BiasValue.cpp
ExtendedLagrangian.cpp
External.cpp
LWalls.cpp
MetaD.cpp
Metainference.cpp
MovingRestraint.cpp
PBMetaD.cpp
Restraint.cpp
ReweightBase.cpp
ReweightBase.h
ReweightBias.cpp
ReweightMetad.cpp
ReweightTemperature.cpp
UWalls.cpp
▶ blas
blas.cpp
blas.h	Header definitions for the standard BLAS library
def_external.h
def_internal.h
simple.h
▶ cltools
▶ config
Config.h
version.h
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ molfile
endianswap.h
fastio.h
Gromacs.h
largefiles.h
libmolfile_plugin.h
molfile_plugin.h
periodic_table.h
readpdb.h
vmdplugin.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ wrapper
Plumed.h
CLTool.cpp
CLTool.h
CLToolRegister.h
Driver.cpp
DriverDouble.cpp
DriverFloat.cpp
GenTemplate.cpp
Info.cpp
kT.cpp
Manual.cpp
SimpleMD.cpp
SumHills.cpp
▶ colvar
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
MultiReferenceBase.h
PointWiseMapping.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionRegister.h
Angle.cpp
Cell.cpp
Colvar.cpp
Colvar.h
Constant.cpp
ContactMap.cpp
Coordination.cpp
CoordinationBase.cpp
CoordinationBase.h
CS2Backbone.cpp
DHEnergy.cpp
Dipole.cpp
Distance.cpp
DRMSD.cpp
Energy.cpp
ERMSD.cpp
Fake.cpp
FretEfficiency.cpp
Gyration.cpp
Jcoupling.cpp
MultiRMSD.cpp
NOE.cpp
PathMSD.cpp
PathMSDBase.cpp
PathMSDBase.h
PCARMSD.cpp
Position.cpp
PRE.cpp
PropertyMap.cpp
Puckering.cpp
RDC.cpp
RMSD.cpp
Template.cpp
Torsion.cpp
Volume.cpp
▶ config
Config.cpp
Config.h
ConfigInstall.cpp
version.h
▶ core
▶ config
Config.h
version.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
Action.cpp
Action.h
ActionAtomistic.cpp
ActionAtomistic.h
ActionPilot.cpp
ActionPilot.h
ActionRegister.cpp
ActionRegister.h
ActionSet.cpp
ActionSet.h
ActionSetup.cpp
ActionSetup.h
ActionWithArguments.cpp
ActionWithArguments.h
ActionWithValue.cpp
ActionWithValue.h
ActionWithVirtualAtom.cpp
ActionWithVirtualAtom.h
Atoms.cpp
Atoms.h
CLTool.cpp
CLTool.h
CLToolMain.cpp
CLToolMain.h
CLToolRegister.cpp
CLToolRegister.h
Colvar.cpp
Colvar.h
ExchangePatterns.cpp
ExchangePatterns.h
FlexibleBin.cpp
FlexibleBin.h
GREX.cpp
GREX.h
MDAtoms.cpp
MDAtoms.h
PlumedMain.cpp
PlumedMain.h
PlumedMainInitializer.cpp
SetupMolInfo.cpp
SetupMolInfo.h
TargetDist.cpp
TargetDist.h
Value.cpp
Value.h
WithCmd.cpp
WithCmd.h
▶ crystallization
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ multicolvar
ActionVolume.h
AtomValuePack.h
BridgedMultiColvarFunction.h
CatomPack.h
MultiColvar.h
MultiColvarBase.h
MultiColvarFilter.h
MultiColvarFunction.h
VolumeGradientBase.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
CubicHarmonicBase.cpp
CubicHarmonicBase.h
Fccubic.cpp
Gradient.cpp
Gradient.h
GradientVessel.cpp
InterMolecularTorsions.cpp
LocalSteinhardt.cpp
LocalSteinhardt.h
MoleculeOrientation.cpp
MoleculePlane.cpp
OrientationSphere.cpp
OrientationSphere.h
Q3.cpp
Q4.cpp
Q6.cpp
SimpleCubic.cpp
SMAC.cpp
Steinhardt.cpp
Steinhardt.h
Tetrahedral.cpp
VectorMean.cpp
VectorMultiColvar.cpp
VectorMultiColvar.h
VectorSum.cpp
▶ function
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
MultiReferenceBase.h
PointWiseMapping.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionRegister.h
Combine.cpp
Ensemble.cpp
FuncPathMSD.cpp
FuncSumHills.cpp
Function.cpp
Function.h
LocalEnsemble.cpp
Matheval.cpp
Piecewise.cpp
Sort.cpp
Stats.cpp
Target.cpp
▶ generic
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
Debug.cpp
DumpAtoms.cpp
DumpDerivatives.cpp
DumpForces.cpp
DumpMassCharge.cpp
DumpProjections.cpp
EffectiveEnergyDrift.cpp
FitToTemplate.cpp
Flush.cpp
Group.cpp
Include.cpp
Print.cpp
RandomExchanges.cpp
Read.cpp
ResetCell.cpp
Time.cpp
UpdateIf.cpp
WholeMolecules.cpp
WrapAround.cpp
▶ gridtools
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
ActionWithGrid.cpp
ActionWithGrid.h
ActionWithInputGrid.cpp
ActionWithInputGrid.h
AverageOnGrid.cpp
AverageOnGrid.h
ContourFindingBase.cpp
ContourFindingBase.h
ConvertToFES.cpp
DumpCube.cpp
DumpGrid.cpp
FindContour.cpp
FindContourSurface.cpp
FindSphericalContour.cpp
FourierTransform.cpp
GridPrintingBase.cpp
GridPrintingBase.h
GridVessel.cpp
GridVessel.h
HistogramOnGrid.cpp
HistogramOnGrid.h
InterpolateGrid.cpp
▶ lapack
▶ blas
blas.h
def_external.h
def_internal.h
simple.h
def_external.h
def_internal.h
lapack.cpp
lapack.h	Header definitions for the standard LAPACK library
lapack_limits.h
simple.h
▶ main
▶ wrapper
Plumed.h
main.cpp
▶ manyrestraints
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
ManyRestraintsBase.cpp
ManyRestraintsBase.h
UWalls.cpp
▶ mapping
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
MultiReferenceBase.h
PointWiseMapping.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
Mapping.cpp
Mapping.h
Path.cpp
PathBase.cpp
PathBase.h
PCAVars.cpp
PropertyMap.cpp
SpathVessel.cpp
ZpathVessel.cpp
▶ molfile
crdplugin.cpp
dcdplugin.cpp
endianswap.h
fastio.h
Gromacs.h
gromacsplugin.cpp
largefiles.h
libmolfile_plugin.h
molfile_plugin.h	API for C extensions to define a way to load structure, coordinate, trajectory, and volumetric data files
pdbplugin.cpp
periodic_table.h
readpdb.h
vmdplugin.h	This header must be included by every VMD plugin library
▶ multicolvar
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ gridtools
ActionWithGrid.h
ActionWithInputGrid.h
AverageOnGrid.h
ContourFindingBase.h
GridPrintingBase.h
GridVessel.h
HistogramOnGrid.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
ActionVolume.cpp
ActionVolume.h
AlphaBeta.cpp
Angles.cpp
AtomValuePack.cpp
AtomValuePack.h
Bridge.cpp
BridgedMultiColvarFunction.cpp
BridgedMultiColvarFunction.h
CatomPack.cpp
CatomPack.h
CenterOfMultiColvar.cpp
CoordinationNumbers.cpp
Density.cpp
DihedralCorrelation.cpp
DistanceFromContour.cpp
Distances.cpp
DumpMultiColvar.cpp
FilterBetween.cpp
FilterLessThan.cpp
FilterMoreThan.cpp
InPlaneDistances.cpp
LocalAverage.cpp
MultiColvar.cpp
MultiColvar.h
MultiColvarBase.cpp
MultiColvarBase.h
MultiColvarDensity.cpp
MultiColvarFilter.cpp
MultiColvarFilter.h
MultiColvarFunction.cpp
MultiColvarFunction.h
NumberOfLinks.cpp
Torsions.cpp
VolumeAround.cpp
VolumeCavity.cpp
VolumeGradientBase.cpp
VolumeGradientBase.h
VolumeInCylinder.cpp
VolumeInSphere.cpp
VolumeTetrapore.cpp
XDistances.cpp
XYDistances.cpp
▶ reference
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ArgumentOnlyDistance.cpp
ArgumentOnlyDistance.h
Direction.cpp
Direction.h
DotProductDistance.cpp
DRMSD.cpp
DRMSD.h
EuclideanDistance.cpp
FakeFrame.cpp
FakeFrame.h
IntermolecularDRMSD.cpp
IntramolecularDRMSD.cpp
MahalanobisDistance.cpp
MetricRegister.cpp
MetricRegister.h
MultiDomainRMSD.cpp
MultiDomainRMSD.h
MultiReferenceBase.cpp
MultiReferenceBase.h
NormalizedEuclideanDistance.cpp
OptimalRMSD.cpp
PointWiseMapping.cpp
PointWiseMapping.h
ReferenceArguments.cpp
ReferenceArguments.h
ReferenceAtoms.cpp
ReferenceAtoms.h
ReferenceConfiguration.cpp
ReferenceConfiguration.h
ReferenceValuePack.cpp
ReferenceValuePack.h
RMSDBase.cpp
RMSDBase.h
SimpleRMSD.cpp
SingleDomainRMSD.cpp
SingleDomainRMSD.h
▶ secondarystructure
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
MultiReferenceBase.h
PointWiseMapping.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
AlphaRMSD.cpp
AntibetaRMSD.cpp
ParabetaRMSD.cpp
SecondaryStructureRMSD.cpp
SecondaryStructureRMSD.h
▶ setup
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionSetup.h
Load.cpp
MolInfo.cpp
Restart.cpp
Units.cpp
▶ tools
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ lapack
def_external.h
def_internal.h
lapack.h
lapack_limits.h
simple.h
Angle.cpp
Angle.h
AtomNumber.cpp
AtomNumber.h
BiasRepresentation.cpp
BiasRepresentation.h
Brent1DRootSearch.cpp
Brent1DRootSearch.h
Citations.cpp
Citations.h
Communicator.cpp
Communicator.h
CubicInterpolation.cpp
CubicInterpolation.h
DLLoader.cpp
DLLoader.h
DynamicList.cpp
DynamicList.h
ERMSD.cpp
ERMSD.h
Exception.cpp
Exception.h
File.h
FileBase.cpp
FileBase.h
Grid.cpp
Grid.h
HistogramBead.cpp
HistogramBead.h
IFile.cpp
IFile.h
Kearsley.cpp
Kearsley.h
KernelFunctions.cpp
KernelFunctions.h
Keywords.cpp
Keywords.h
LatticeReduction.cpp
LatticeReduction.h
LinkCells.cpp
LinkCells.h
Log.cpp
Log.h
LoopUnroller.cpp
LoopUnroller.h
Matrix.cpp
Matrix.h
MatrixSquareBracketsAccess.cpp
MatrixSquareBracketsAccess.h
Minimise1DBrent.cpp
Minimise1DBrent.h
MinimiseBase.cpp
MinimiseBase.h
MolDataClass.cpp
MolDataClass.h
MultiValue.cpp
MultiValue.h
NeighborList.cpp
NeighborList.h
OFile.cpp
OFile.h
OpenMP.cpp
OpenMP.h
OptimalAlignment.cpp
OptimalAlignment.h
Pbc.cpp
Pbc.h
PDB.cpp
PDB.h
Random.cpp
Random.h
RMSD.cpp
RMSD.h
RootFindingBase.cpp
RootFindingBase.h
Stopwatch.cpp
Stopwatch.h
SwitchingFunction.cpp
SwitchingFunction.h
Tensor.cpp
Tensor.h
Tools.cpp
Tools.h
Torsion.cpp
Torsion.h
Units.cpp
Units.h
Vector.cpp
Vector.h
▶ vatom
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionRegister.h
ActionWithVirtualAtom.cpp
ActionWithVirtualAtom.h
Center.cpp
COM.cpp
FixedAtom.cpp
Ghost.cpp
▶ vesselbase
▶ core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionWithAveraging.cpp
ActionWithAveraging.h
ActionWithInputVessel.cpp
ActionWithInputVessel.h
ActionWithVessel.cpp
ActionWithVessel.h
AltMin.cpp
AveragingVessel.cpp
AveragingVessel.h
Between.cpp
Between.h
BridgeVessel.cpp
BridgeVessel.h
FunctionVessel.cpp
FunctionVessel.h
Highest.cpp
Histogram.cpp
LessThan.cpp
LessThan.h
Lowest.cpp
Max.cpp
Mean.cpp
Min.cpp
Moments.cpp
MoreThan.cpp
OrderingVessel.cpp
OrderingVessel.h
ShortcutVessel.cpp
ShortcutVessel.h
StoreDataVessel.cpp
StoreDataVessel.h
Sum.cpp
ValueVessel.cpp
ValueVessel.h
Vessel.cpp
Vessel.h
VesselRegister.cpp
VesselRegister.h
▶ wrapper
Plumed.c
Plumed.h
PlumedStatic.cpp