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  A  
Flush (PLMD::generic)   PropertyMap (PLMD::mapping)   
FuncPathMSD (PLMD::function)   Puckering (PLMD::colvar)   
ABMD (PLMD::bias)   FuncSumHills (PLMD::function)   
  Q  
Action (PLMD)   Function (PLMD::function)   
ActionAtomistic (PLMD)   FunctionVessel (PLMD::vesselbase)   Q3 (PLMD::crystallization)   
ActionOptions (PLMD)   
  G  
Q4 (PLMD::crystallization)   
ActionPilot (PLMD)   Q6 (PLMD::crystallization)   
ActionRegister (PLMD)   MetaD::Gaussian (PLMD::bias)   
  R  
ActionSet (PLMD)   GenTemplate (PLMD::cltools)   
ActionSetup (PLMD)   Ghost (PLMD::vatom)   Random (PLMD)   
ActionVolume (PLMD::multicolvar)   Gradient (PLMD::crystallisation)   RandomExchanges (PLMD::generic)   
ActionWithArguments (PLMD)   GradientVessel (PLMD::crystallisation)   RDC (PLMD)   
ActionWithInputMatrix (PLMD::adjmat)   GREX (PLMD)   Read (PLMD::generic)   
ActionWithInputVessel (PLMD::vesselbase)   Grid (PLMD)   ReferenceArguments (PLMD)   
ActionWithValue (PLMD)   Group (PLMD::generic)   ReferenceAtoms (PLMD)   
ActionWithVessel (PLMD::vesselbase)   Gyration (PLMD::colvar)   ReferenceConfiguration (PLMD)   
ActionWithVirtualAtom (PLMD)   
  H  
ReferenceConfigurationOptions (PLMD)   
AdjacencyMatrixBase (PLMD::adjmat)   ReferenceValuePack (PLMD)   
AdjacencyMatrixVessel (PLMD::adjmat)   HBondMatrix (PLMD::adjmat)   Communicator::Request (PLMD)   
AlphaBeta (PLMD::multicolvar)   Highest (PLMD::vesselbase)   Restart (PLMD::setup)   
AlphaRMSD (PLMD::secondarystructure)   Histogram (PLMD::analysis)   Restraint (PLMD::bias)   
AltMin (PLMD::mapping)   Histogram (PLMD::vesselbase)   RMSD (PLMD::colvar)   
Analysis (PLMD::analysis)   HistogramBead (PLMD)   RMSD (PLMD)   
AnalysisWithLandmarks (PLMD::analysis)   
  I  
RMSDBase (PLMD)   
Angle (PLMD::colvar)   RMSDCoreData (PLMD)   
Angle (PLMD)   IFile (PLMD)   MatrixSquareBracketsAccess::Row (PLMD)   
Angles (PLMD::multicolvar)   PathMSDBase::ImagePath (PLMD::colvar)   
  S  
AntibetaRMSD (PLMD::secondarystructure)   IMD (PLMD)   
ArgumentOnlyDistance (PLMD)   Include (PLMD::generic)   SecondaryStructureRMSD (PLMD::secondarystructure)   
AtomNumber (PLMD)   Info (PLMD::cltools)   SetupMolInfo (PLMD)   
Atoms (PLMD)   InPlaneDistances (PLMD::multicolvar)   ShortcutVessel (PLMD::vesselbase)   
AtomValuePack (PLMD::multicolvar)   InterpolateBicubic (PLMD)   SimpleCubic (PLMD::crystallization)   
  B  
InterpolateCubic (PLMD)   SimpleMD (PLMD::cltools)   
  K  
SimpleRMSD (PLMD)   
Between (PLMD::vesselbase)   SingleDomainRMSD (PLMD)   
Bias (PLMD::bias)   Kearsley (PLMD)   SMAC (PLMD::crystallization)   
BiasRepresentation (PLMD)   KernelFunctions (PLMD)   Sort (PLMD::function)   
BiasValue (PLMD::bias)   Keywords::KeyType (PLMD)   SparseGrid (PLMD)   
BiasWeight (PLMD)   Keywords (PLMD)   SpathVessel (PLMD::mapping)   
Bridge (PLMD::multicolvar)   
  L  
Sprint (PLMD::adjmat)   
BridgedMultiColvarFunction (PLMD::multicolvar)   Communicator::Status (PLMD)   
BridgeVessel (PLMD::vesselbase)   LandmarkRegister (PLMD::analysis)   Steinhardt (PLMD::crystallization)   
  C  
LandmarkSelectionBase (PLMD::analysis)   Stopwatch (PLMD)   
LandmarkSelectionOptions (PLMD::analysis)   StoreDataVessel (PLMD::vesselbase)   
CatomPack (PLMD::multicolvar)   LatticeReduction (PLMD)   Sum (PLMD::vesselbase)   
Cell (PLMD::colvar)   LessThan (PLMD::vesselbase)   SwitchingFunction (PLMD)   
Center (PLMD::vatom)   LinkCells (PLMD)   
  T  
CH3Shifts (PLMD)   Load (PLMD::setup)   
CInterpolation (PLMD)   LOCAL_Q3 (PLMD::crystallization)   Target (PLMD::function)   
Citations (PLMD)   LOCAL_Q4 (PLMD::crystallization)   TargetDist (PLMD)   
ClassicalMultiDimensionalScaling (PLMD::analysis)   LOCAL_Q6 (PLMD::crystallization)   Template (PLMD::colvar)   
ClassicalScaling (PLMD::analysis)   LocalAverage (PLMD::multicolvar)   TensorChecks (PLMD)   
CLTool (PLMD)   LocalSteinhardt (PLMD::crystallization)   TensorGeneric (PLMD)   
CLToolMain (PLMD)   Log (PLMD)   Tetrahedral (PLMD::crystallization)   
CLToolOptions (PLMD)   LoopUnroller (PLMD)   Stopwatch::Time (PLMD)   
CLToolRegister (PLMD)   Lowest (PLMD::vesselbase)   Time (PLMD::generic)   
CLToolSumHills (PLMD::cltools)   LWalls (PLMD::bias)   Tools (PLMD)   
Colvar (PLMD)   
  M  
Torsion (PLMD)   
ColvarFake (PLMD::colvar)   Torsion (PLMD::colvar)   
COM (PLMD::vatom)   MahalanobisDistance (PLMD)   Torsions (PLMD::multicolvar)   
Combine (PLMD::function)   Manual (PLMD::cltools)   
  U  
Committor (PLMD::analysis)   ManyRestraintsBase (PLMD::manyrestraints)   
Communicator (PLMD)   Mapping (PLMD::mapping)   Units (PLMD)   
MatrixSquareBracketsAccess::Const_row (PLMD)   Matheval (PLMD::function)   Units (PLMD::setup)   
Constant (PLMD::colvar)   Matrix (PLMD)   UWalls (PLMD::manyrestraints)   
Communicator::ConstData (PLMD)   MatrixColumnSums (PLMD::adjmat)   UWalls (PLMD::bias)   
ContactAlignedMatrix (PLMD::adjmat)   MatrixRowSums (PLMD::adjmat)   
  V  
ContactMap (PLMD::colvar)   MatrixSquareBracketsAccess (PLMD)   
ContactMatrix (PLMD::adjmat)   MatrixSummationBase (PLMD::adjmat)   Value (PLMD)   
Coordination (PLMD::colvar)   Max (PLMD::vesselbase)   ValueVessel (PLMD::vesselbase)   
CoordinationBase (PLMD::colvar)   MDAtomsBase (PLMD)   VectorChecks (PLMD)   
CoordinationNumbers (PLMD::multicolvar)   MDAtomsTyped (PLMD)   VectorGeneric (PLMD)   
CopyAllFrames (PLMD::analysis)   Mean (PLMD::vesselbase)   VectorMean (PLMD::crystallization)   
CS2Backbone (PLMD)   MetaD (PLMD::bias)   VectorMultiColvar (PLMD::crystallization)   
  D  
MetricRegister (PLMD)   VectorSum (PLMD::crystallization)   
Min (PLMD::vesselbase)   Vessel (PLMD::vesselbase)   
Communicator::Data (PLMD)   MolDataClass (PLMD)   VesselOptions (PLMD::vesselbase)   
Debug (PLMD::generic)   MoleculeOrientation (PLMD::crystallization)   VesselRegister (PLMD::vesselbase)   
Density (PLMD::multicolvar)   MoleculePlane (PLMD::crystallization)   Volume (PLMD::colvar)   
DFSBase (PLMD::adjmat)   MolInfo (PLMD::setup)   VolumeAround (PLMD::multicolvar)   
DFSBasic (PLMD::adjmat)   Moments (PLMD::vesselbase)   VolumeCavity (PLMD::multicolvar)   
DFSBasicWithSurface (PLMD::adjmat)   MoreThan (PLMD::vesselbase)   VolumeGradientBase (PLMD::multicolvar)   
DFSClusterDiameter (PLMD::adjmat)   MovingRestraint (PLMD::bias)   VolumeInCylinder (PLMD::multicolvar)   
DFSMaxCluster (PLMD::adjmat)   MPI_Comm (PLMD)   VolumeInSphere (PLMD::multicolvar)   
DFSNumberOfClusters (PLMD::adjmat)   MPI_Datatype (PLMD)   VolumeTetrapore (PLMD::multicolvar)   
DFSOutput (PLMD::adjmat)   MPI_Request (PLMD)   
  W  
DHEnergy (PLMD::colvar)   MPI_Status (PLMD)   
DihedralCorrelation (PLMD::multicolvar)   MultiColvar (PLMD::multicolvar)   Stopwatch::Watch (PLMD)   
Dipole (PLMD::colvar)   MultiColvarBase (PLMD::multicolvar)   WeightBase (PLMD)   
Direction (PLMD)   MultiColvarDensity (PLMD::multicolvar)   WholeMolecules (PLMD::generic)   
Distance (PLMD::colvar)   MultiColvarFilter (PLMD::multicolvar)   WithCmd (PLMD)   
Distances (PLMD::multicolvar)   MultiColvarFunction (PLMD::multicolvar)   WrapAround (PLMD::generic)   
DLLoader (PLMD)   MultiDomainRMSD (PLMD)   
  X  
Atoms::DomainDecomposition (PLMD)   MultiReferenceBase (PLMD)   
DotProductDistance (PLMD)   MultiRMSD (PLMD::colvar)   XDistances (PLMD::multicolvar)   
Driver (PLMD::cltools)   MultiValue (PLMD)   XYDistances (PLMD::multicolvar)   
DRMSD (PLMD)   
  N  
  Z  
DRMSD (PLMD::colvar)   
DumpAtoms (PLMD::generic)   NeighborList (PLMD)   ZpathVessel (PLMD::mapping)   
DumpDerivatives (PLMD::generic)   NOE (PLMD::colvar)   
  f  
DumpForces (PLMD::generic)   NormalizedEuclideanDistance (PLMD)   
DumpMassCharge (PLMD::generic)   NumberOfLinks (PLMD::multicolvar)   fio_iovec (PLMD::molfile)   
DumpMultiColvar (PLMD::multicolvar)   
  O  
  i  
DumpProjections (PLMD::generic)   
DynamicList (PLMD)   OFile (PLMD)   PathMSDBase::imgOrderByDist (PLMD::colvar)   
  E  
OpenMP (PLMD)   PathMSDBase::imgOrderBySimilarity (PLMD::colvar)   
OptimalAlignment (PLMD)   
  k  
EffectiveEnergyDrift (PLMD::generic)   OptimalRMSD (PLMD)   
Energy (PLMD::colvar)   OrderingVessel (PLMD::vesselbase)   kt (PLMD::cltools)   
Ensemble (PLMD::function)   OrientationSphere (PLMD::crystallization)   
  m  
EuclideanDistance (PLMD)   
  P  
Exception (PLMD)   md_atom (PLMD::molfile)   
ExchangePatterns (PLMD)   ParabetaRMSD (PLMD::secondarystructure)   md_box (PLMD::molfile)   
ExtendedLagrangian (PLMD::bias)   Path (PLMD::mapping)   md_file (PLMD::molfile)   
External (PLMD::bias)   PathBase (PLMD::mapping)   md_header (PLMD::molfile)   
  F  
PathMSD (PLMD::colvar)   md_ts (PLMD::molfile)   
PathMSDBase (PLMD::colvar)   molfile_atom_t (PLMD::molfile)   
FakeFrame (PLMD)   Pbc (PLMD)   molfile_graphics_t (PLMD::molfile)   
Fccubic (PLMD::crystallization)   PCARMSD (PLMD::colvar)   molfile_metadata_t (PLMD::molfile)   
IFile::Field (PLMD)   PCAVars (PLMD::mapping)   molfile_plugin_t (PLMD::molfile)   
OFile::Field (PLMD)   PDB (PLMD)   molfile_qm_basis_t (PLMD::molfile)   
FileBase::FieldBase (PLMD)   Piecewise (PLMD::function)   molfile_qm_hessian_t (PLMD::molfile)   
FileBase (PLMD)   Plumed (PLMD)   molfile_qm_metadata_t (PLMD::molfile)   
FilesHandler (PLMD::function)   PlumedMain (PLMD)   molfile_qm_sysinfo_t (PLMD::molfile)   
FilterBetween (PLMD::multicolvar)   PlumedMainInitializer (PLMD)   molfile_qm_t (PLMD::molfile)   
FilterLess (PLMD::multicolvar)   PointWiseMapping (PLMD)   molfile_qm_timestep_metadata (PLMD::molfile)   
FilterMore (PLMD::multicolvar)   Position (PLMD::colvar)   molfile_qm_timestep_t (PLMD::molfile)   
FitToTemplate (PLMD::generic)   Print (PLMD::generic)   molfile_qm_wavefunction_t (PLMD::molfile)   
FixedAtom (PLMD::vatom)   ProbWeight (PLMD)   molfile_timestep_metadata (PLMD::molfile)   
FlexibleBin (PLMD)   PropertyMap (PLMD::colvar)   molfile_timestep_t (PLMD::molfile)   
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