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NAMD Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
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ABoundAngleRestraint
ABoundDiheRestraint
ABoundDistRestraint
ABoundPosRestraint
ADiheRestraint
ADistRestraint
AFixedAngleRestraint
AFixedDiheRestraint
AFixedDistRestraint
AFixedPosRestraint
AForcingAngleRestraint
AForcingDiheRestraint
AForcingDistRestraint
AForcingPosRestraint
AGroup
ALambdaControl
ALambdaManager
Alg7
AlgNbor
AlgRecBisection
AlignVector
AnAngleRestraint
angle
angle_params
AngleElem
AngleTable
AngleValue
aniso
AnisoElem
APosRestraint
ARestraint
ARestraintManager
msm::Array< T >
Array< Elem, Size >
atom_constants
atom_name_info
msm::AtomCoord
AtomCstInfo
atomID_less
AtomMap
AtomMapper
AtomNameIdx
AtomsCntPerPatchMsg
AtomSigInfo
AtomSignature
AtomTable
AVector
BackEnd
BasicAtomInfo
msm::BlockDiagram
msm::BlockIndex
msm::BlockSend
BOCclass
BOCgroup
BOID
bond
bond_params
BondElem
BondTable
BondValue
Box< Owner, Data >
BroadcastClient
BroadcastClientElem
BroadcastMgr
BroadcastMsg
C1Matrix
C1Vector
CBase_OptPmeXPencil
CBase_OptPmeYPencil
CBase_OptPmeZPencil
CBase_PmeXPencil
CBase_PmeYPencil
CBase_PmeZPencil
CkCallbackWrapper
ClusterCoorElem
ClusterCoorMsg
ClusterElem
ClusterSizeMsg
CollectionMaster
CollectionMaster::CollectVectorInstance
CollectionMaster::CollectVectorSequence
CollectionMgr
CollectionMgr::CollectVectorInstance
CollectionMgr::CollectVectorSequence
CollectVectorMsg
CollectVectorVarMsg
colvarA collective variable (main class); to be defined, it needs at least one object of a derived class of colvar::cvc; it calculates and returns a object
colvar::alpha_anglesColvar component: alpha helix content of a contiguous segment of 5 or more residues, implemented as a sum of phi/psi dihedral angles and hydrogen bonds (colvarvalue::type_scalar type, range [0:1]) Colvar component: alpha helix content of a contiguous segment of 5 or more residues, implemented as a sum of Ca-Ca-Ca angles and hydrogen bonds (colvarvalue::type_scalar type, range [0:1])
colvar::angleColvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI])
colvar::coordnumColvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2])
colvar::cvcColvar component (base class); most implementations of utilize one or more or objects to access atoms
colvar::dihedPCColvar component: dihedPC Projection of the config onto a dihedral principal component See e.g. Altis et al., J. Chem. Phys 126, 244111 (2007) Based on a set of 'dihedral' cvcs
colvar::dihedralColvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI])
colvar::distanceColvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*))
colvar::distance_dirColvar component: distance unit vector (direction) between centers of mass of two groups (colvarvalue::type_unitvector type, range [-1:1]x[-1:1]x[-1:1])
colvar::distance_invColvar component: average distance between two groups of atoms, weighted as the sixth power, as in NMR refinements (colvarvalue::type_scalar type, range (0:*))
colvar::distance_vec
colvar::distance_xyColvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*))
colvar::distance_zColvar component: projection of the distance vector along an axis (colvarvalue::type_scalar type, range (-*:*))
colvar::eigenvectorColvar component: projection of 3N coordinates onto an eigenvector (colvarvalue::type_scalar type, range (-*:*))
colvar::gyrationColvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*))
colvar::h_bondColvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol)) (colvarvalue::type_scalar type, range [0:1])
colvar::inertiaColvar component: moment of inertia of an atom group (colvarvalue::type_scalar type, range [0:*))
colvar::inertia_zColvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_scalar type, range [0:*))
colvar::orientationColvar component: orientation in space of an atom group, with respect to a set of reference coordinates (colvarvalue::type_quaternion type, range [-1:1]x[-1:1]x[-1:1]x[-1:1])
colvar::orientation_angleColvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [0:PI))
colvar::rmsdColvar component: root mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses to calculate the rotation matrix (colvarvalue::type_scalar type, range [0:*))
colvar::selfcoordnumColvar component: self-coordination number within a group (colvarvalue::type_scalar type, range [0:N*(N-1)/2])
colvar::spin_angleColvar component: angle of rotation around a predefined axis (colvarvalue::type_scalar type, range [-PI:PI])
colvar::tiltColvar component: projection of the orientation vector onto a predefined axis (colvarvalue::type_scalar type, range [-1:1])
colvar_grid< T >Grid of values of a function of several collective variables
colvar_grid_countColvar_grid derived class to hold counters in discrete n-dim colvar space
colvar_grid_gradientClass for accumulating the gradient of a scalar function on a grid
colvar_grid_scalarClass for accumulating a scalar function on a grid
colvarbiasCollective variable bias, base class
colvarbias_abfABF bias
colvarbias_harmonicHarmonic restraint, optionally moving towards a target (implementation of )
colvarbias_histogramHistogram "bias" (does as the name says)
colvarbias_metaMetadynamics bias (implementation of )
colvarbias_meta::hillA hill for the metadynamics bias
colvarmoduleCollective variables module (main class)
colvarmodule::atomStores numeric id, mass and all mutable data for an atom, mostly used by a
colvarmodule::atom_groupGroup of objects, mostly used by a
colvarmodule::matrix2d< T, outer_length, inner_length >Arbitrary size array (two dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions)
colvarmodule::quaternion1-dimensional vector of real numbers with four components and a quaternion algebra
colvarmodule::rmatrix2-dimensional array of real numbers with three components along each dimension (works with colvarmodule::rvector)
colvarmodule::rotationA rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion)
colvarmodule::rvector1-dimensional vector of real numbers with three components
colvarmodule::vector1d< T, length >Arbitrary size array (one dimensions) suitable for linear algebra operations (i.e. for floating point numbers it can be used with library functions)
colvarparse
colvarparse::read_blockHelper class to read a block of the type "key { ... }" from a stream and store it in a string
colvarproxyInterface class between the collective variables module and the simulation program
colvarproxy_namdCommunication between colvars and NAMD (implementation of )
colvarvalueValue of a collective variable: this is a metatype which can be set at runtime. By default it is set to be a scalar number, and can be treated like that in all operations (this is done by most implementations)
Communicate
CompAtom
CompAtomExt
Compute
ComputeAngles
ComputeAniso
ComputeBonds
ComputeConsForce
ComputeConsForceMsg
ComputeConsTorque
ComputeCrossterms
ComputeCylindricalBC
ComputeDihedrals
ComputeDPMEDataMsg
ComputeDPMEResultsMsg
ComputeEField
ComputeEwald
ComputeEwaldMsg
ComputeExcls
ComputeExt
ComputeExtAtom
ComputeExtMgr
ComputeFmmSerial
ComputeFmmSerialAtom
ComputeFmmSerialMgr
ComputeFullDirect
ComputeGBISAtom
ComputeGBISser
ComputeGBISserMgr
ComputeGlobal
ComputeGlobalDataMsg
ComputeGlobalResultsMsg
ComputeGridForce
ComputeHomePatch
ComputeHomePatches
ComputeHomeTuples< T, S, P >
ComputeImpropers
computeInfo
ComputeLCPO
ComputeMap
ComputeMap::ComputeData
ComputeMap::PatchRec
ComputeMapChangeMsg
ComputeMapMsg
ComputeMgr
ComputeMoa
ComputeMsm
ComputeMsmMgr
ComputeMsmSerial
ComputeMsmSerialAtom
ComputeMsmSerialMgr
ComputeNonbondedCUDA
ComputeNonbondedCUDA::compute_record
ComputeNonbondedCUDA::patch_record
ComputeNonbondedPair
ComputeNonbondedSelf
ComputeNonbondedUtil
ComputeNonbondedWorkArrays
ComputePatch
ComputePatchPair
ComputePme
ComputePmeMgr
ComputeRestraints
ComputeSelfAngles
ComputeSelfAniso
ComputeSelfBonds
ComputeSelfCrossterms
ComputeSelfDihedrals
ComputeSelfExcls
ComputeSelfImpropers
ComputeSelfThole
ComputeSelfTuples< T, S, P >
ComputeSphericalBC
ComputeStir
ComputeTclBC
ComputeThole
ConfigList
ConfigList::ConfigListNode
Controller
ControllerBroadcasts
cr_sortop
crossterm
crossterm_params
CrosstermData
CrosstermElem
CrosstermValue
CudaAtom
DataExchanger
DataMessage
datastream
DataStreamMsg
dihedral
dihedral_params
DihedralElem
DihedralTable
DihedralValue
doublecomplex
drude_constants
Entry< Elem >
EntryGlob< Elem >
EwaldParticle
ExclElem
ExclSigInfo
Exclusion
ExclusionCheck
ExclusionSignature
exlist_sortop
ExtCoordMsg
ExtForce
ExtForceMsg
FileStack
Flags
floatcomplex
FloatVector
FmmSerialCoordMsg
FmmSerialForceMsg
msm::FoldFactor
four_body_consts
FullAtom
GBISCoordMsg
GBISForceMsg
GBISParamStruct
GenericAngle
GenericAtom
GenericBond
GenericDihedral
GenericMol
GlobalMaster
GlobalMasterEasy
GlobalMasterFreeEnergy
GlobalMasterIMD
GlobalMasterMisc
GlobalMasterServer
GlobalMasterSMD
GlobalMasterSymmetry
GlobalMasterTcl
GlobalMasterTest
GlobalMasterTMD
go_pair
go_val
msm::Grid< T >
msm::GridFixed< T, N >
GridforceFullBaseGrid
GridforceFullBaseGrid::GridIndices
GridforceFullMainGrid
GridforceFullSubGrid
GridforceGrid
GridforceLiteGrid
GridMsg
GroGaussPair
GroLJPair
GromacsTopFile
GroupInitMsg
HashPool< T >
HashPoolAdaptorT< T >
HashReal
HashString
heapIterator
heapRecord
HomePatch
HomePatchElem
HydroBasedMsg
HydrogenGroupID
ijpair
ijpair_sortop_bit_reversed
IMDEnergies
IMDheader
IMDOutput
improper
improper_params
ImproperElem
ImproperValue
indexed_nbthole_pair
indexed_table_pair
indexed_vdw_pair
msm::IndexRange
InfoRecord
infostream
InputAtom
Int2
Int3
InterpParams_t
IRSet
Iterator
msm::Ivec
LargeIRSet
Lattice
LCPOAtom
LCPONeighborList
LdbCoordinator
LdbMigrateMsg
listNode
LJTable
LJTable::TableEntry
LocalID
LocalLBInfoMsg
LocalPmeInfo
LocalWorkMsg
lphost
main
msm::Map
MathArray< Elem, Size >
Matrix44x4 matrix class with numerous operators, conversions, etc
Matrix4Symmetry
Matrix4TMD
maxHeap
Measure
memusageinit
MGridforceParams
MGridforceParamsList
MigrateAtomsCombinedMsg
MigrateAtomsMsg
MigrationInfo
minHeap
minpoint
MIStream
MoaData
Molecule
MolInfoMsg
MolInst
MOStream
MoveAllByMsg
MoveAtomMsg
MoveInputAtomsMsg
MovePatch
MovePatchAtomsMsg
MovePatchesMsg
MsmBlock
MsmBlockKernel< Vtype, Mtype >
MsmBlockMap
MsmBlockProxyMsg
MsmC1HermiteBlock
MsmC1HermiteBlockProxyMsg
MsmC1HermiteGridCutoff
MsmC1HermiteGridCutoffProxyMsg
MsmC1HermiteGridCutoffSetupMsg
MsmGridCutoff
MsmGridCutoffInitMsg
MsmGridCutoffKernel< Vtype, Mtype >
MsmGridCutoffMap
MsmGridCutoffProxyMsg
MsmGridCutoffSetupMsg
MsmInitMsg
MsmProfiler
MsmSerialCoordMsg
MsmSerialForceMsg
MsmTimer
NamdCentLB
NamdDummyLB
NamdHybridLB
NamdNborLB
NamdState
nbthole_pair_params
nbthole_pair_value
netintStructure used to perform byte swapping operations
NL_Msm_t
Node
NodePmeInfo
NodePmeMgr
NodeProxyMgr
nodesort
nonbonded
NonbondedCUDASlaveMsg
NonbondedExclValue
ObjectArena< Type >
OptPmeCompute
OptPmeDummyMsg
OptPmeFFTMsg
OptPmeGridMsg
OptPmeMgr
OptPmePencil< T >
OptPmePencilInitMsg
OptPmePencilInitMsgData
OptPmePencilMapX
OptPmePencilMapY
OptPmePencilMapZ
OptPmeRealSpace
OptPmeSubComputeMsg
OptPmeXPencil
OptPmeYPencil
OptPmeZPencil
Output
OutputAtomRecord
OutputAtomRecord::floatVals
OutputAtomRecord::integerVals
OutputAtomRecord::shortVals
OwnerBox< Owner, Data >
Pairlists
PairTable
PAL
ParallelIOMgr
Parameters
parm
ParseOptions
ParseOptions::DataElement
Patch
patch_sortop_curve_a
patch_sortop_curve_b
patch_sortop_curve_c
msm::PatchData
msm::PatchDiagram
PatchElem
PatchGridElem
patchInfo
PatchMap
PatchMapMsg
PatchMgr
PatchProxyListMsg
msm::PatchSend
PDB
PDBAtom
PDBAtomRecord
PDBData
PDBHetatm
PDBUnknown
pe_sortop_bit_reversed
pe_sortop_coord_x
pe_sortop_coord_y
PencilElement
PluginIOMgr
PmeAckMsg
PmeFFTInfo
PmeGrid
PmeGridMsg
PmeKSpace
PmeParticle
PmePencil< T >
PmePencilInitMsg
PmePencilInitMsgData
PmePencilMap
PmeRealSpace
PmeSharedTransMsg
PmeSharedUntransMsg
PmeTransMsg
PmeUntransMsg
PmeXPencil
PmeYPencil
PmeZPencil
Pointer
position_index
PressureProfileReduction
msm::PriorityQueue< T >
processorInfo
ProxyCombinedResultMsg
ProxyCombinedResultRawMsg
ProxyDataMsg
ProxyElem
ProxyGBISP1ResultMsg
ProxyGBISP2DataMsg
ProxyGBISP2ResultMsg
ProxyGBISP3DataMsg
ProxyListInfo
ProxyMgr
ProxyNodeAwareSpanningTreeMsg
ProxyPatch
ProxyResultMsg
ProxyResultVarsizeMsg
ProxySpanningTreeMsg
ProxyTree
proxyTreeNode
ProxyUsage
ProxyUsageKey
Random
Rebalancer
Rebalancer::pcpair
RecBisection
ReductionMgr
ReductionRegisterMsg
ReductionSet
ReductionSetData
ReductionSubmitMsg
RefineOnly
RefineTorusLB
RegisterProxyMsg
RequireReduction
ResidueLookupElem
ResizeArray< Elem >
ResizeArrayIter< T >
ResizeArrayPrimIter< T >
ResizeArrayRaw< Elem >
Results
ScriptParamMsg
ScriptTcl
seg_resid
Sequencer
SetLatticeMsg
SimParameters
SimpleBroadcastObject< T >
SlaveInitMsg
SortableResizeArray< Elem >
SortedArray< Elem >
sortop_base
sortop_bit_reversed
sortop_x
sortop_y
sortop_z
StreamMessage
StringList
SubmitReduction
Sync
table_pair_params
TaggedMsg
Tensor
thole
TholeElem
TorusLB
Transform
TuplePatchElem
TupleSignature
UniqueSet< Elem >
UniqueSetIter< T >
UniqueSetRaw< Elem >
UniqueSortedArray< Elem >
UnregisterProxyMsg
vdw_pair_params
vdw_params
vdw_val
VDWTable
vect
Vector
vmdforce
wkf_timer
wkfmsgtimer
WorkDistrib
WorkDistrib::pe_sortop_compact
WorkDistrib::pe_sortop_diffuse
WorkIndex
zVector

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