Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 12]

AmberParm7Reader
FortranFormatSpecifier
FortranData
Ambertoppar
eabffunc
msm
PatchData
Array
PriorityQueue
Ivec
IndexRange
Grid
GridFixed
BlockIndex
FoldFactor
BlockSend
PatchSend
PatchDiagram
BlockDiagram
Map
AtomCoord
__sort_entry
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
Array
assert_ProxyResultVarsizeMsg
atom_constants
atom_name_info
AtomCstInfo
atomID_less
AtomMap
AtomMapper
AtomNameIdx
AtomsCntPerPatchMsg
AtomSigInfo
AtomSignature
AtomTable
AVector
BackEnd
BasicAtomInfo
BOCgroup
BOID
bond
bond_params
BondElem
BondTable
BondValue
BoundingBox
Box
BroadcastClient
BroadcastClientElem
BroadcastMgr
BroadcastMsg
C1Matrix
C1Vector
CheckpointAtomsMsg
CheckpointAtomsReqMsg
CheckpointMsg
CkPrintf_stringbuf
ClusterCoorElem
ClusterCoorMsg
ClusterElem
ClusterSizeMsg
CollectionMaster
CollectVectorInstance
CollectVectorSequence
CollectionMgr
CollectVectorInstance
CollectVectorSequence
CollectLoadsMsg
CollectProxyVectorInstance
CollectProxyVectorSequence
CollectVectorMsg
CollectVectorVarMsg
colvarproxy_namd	Communication between colvars and NAMD (implementation of colvarproxy)
Communicate
CompAtom
CompAtomExt
Compute
ComputeAngles
ComputeAniso
ComputeBondedCUDAKernel
BondedVirial
ComputeBonds
ComputeConsForce
ComputeConsForceMsg
ComputeConsTorque
ComputeCrossterms
ComputeCUDAMgr
ComputeCylindricalBC
ComputeDihedrals
ComputeDPMEDataMsg
ComputeDPMEResultsMsg
ComputeEField
ComputeEwald
ComputeEwaldMsg
ComputeExcls
ComputeExt
ComputeExtAtom
ComputeExtMgr
ComputeFmmSerial
ComputeFmmSerialAtom
ComputeFmmSerialMgr
ComputeFullDirect
ComputeGBISAtom
ComputeGBISser
ComputeGBISserMgr
ComputeGlobal
ComputeGlobalDataMsg
ComputeGlobalResultsMsg
ComputeGridForce
ComputeGromacsPair
ComputeHomePatch
ComputeHomePatches
ComputeHomeTuples
ComputeImpropers
computeInfo
ComputeLCPO
ComputeMap
ComputeData
PatchRec
ComputeMapChangeMsg
ComputeMgr
ComputeMoa
ComputeMsm
ComputeMsmMgr
ComputeMsmSerial
ComputeMsmSerialAtom
ComputeMsmSerialMgr
ComputeNonbondedCUDA
compute_record
patch_record
ComputeNonbondedMIC
compute_record
patch_record
ComputeNonbondedPair
ComputeNonbondedSelf
ComputeNonbondedUtil
ComputeNonbondedWorkArrays
ComputePatch
ComputePatchPair
ComputePme
ComputePmeCUDA
ComputePmeCUDADevice
ComputePmeCUDAMgr
ComputePmeMgr
cuda_submit_charges_args
ComputePmeUtil
ComputeQM
ComputeQMAtom
ComputeQMMgr
ComputeQMPntChrg
ComputeRestraints
ComputeSelfAngles
ComputeSelfAniso
ComputeSelfBonds
ComputeSelfCrossterms
ComputeSelfDihedrals
ComputeSelfExcls
ComputeSelfGromacsPair
ComputeSelfImpropers
ComputeSelfThole
ComputeSelfTuples
ComputeSphericalBC
ComputeStir
ComputeTclBC
ComputeThole
ConfigList
ConfigListNode
ConstPointer
Controller
checkpoint
ControllerBroadcasts
ControllerState
cptr_sortop_priority
CpuPmeAtomStorage
cr_sortop_distance
cr_sortop_reverse_priority
crossterm
crossterm_params
CrosstermData
CrosstermElem
CrosstermValue
cuda_args_t
CudaAngle
CudaAngleValue
CudaAtom
CudaBond
CudaBondValue
CudaComputeGBISKernel
CudaComputeNonbonded
ComputeRecord
PatchRecord
CudaComputeNonbondedKernel
CudaComputeNonbondedMsg
CudaComputeRecord
CudaCrossterm
CudaCrosstermValue
CudaDihedral
CudaDihedralValue
CudaExclusion
CudaFFTCompute
CudaForce
CudaNonbondedTables
CudaPatchRecord
CudaPmeAtomStorage
CudaPmeKSpaceCompute
CudaPmePencilX
CudaPmePencilXY
CudaPmePencilXYZ
CudaPmePencilY
CudaPmePencilZ
CudaPmeRealSpaceCompute
CudaPmeTranspose
CudaPmeXInitMsg
CudaPmeXYInitMsg
CudaPmeXYZInitMsg
CudaStaticAssert
CudaStaticAssert< true >
CudaTileListKernel
DataExchanger
DataMessage
datastream
DataStreamMsg
DeviceBuffer
DeviceCUDA
DeviceDataMsg
dihedral
dihedral_params
DihedralElem
DihedralTable
DihedralValue
doublecomplex
drude_constants
dummyData
eABF
eABF1D
eABF2D
Entry
EntryGlob
EwaldParticle
ExchangeAtomsMsg
ExchangeAtomsReqMsg
ExclElem
exclmask
ExclSigInfo
Exclusion
ExclusionCheck
ExclusionSignature
exlist_sortop
ExtCoordMsg
ExtForce
ExtForceMsg
FFTCompute
FileStack
FinishWorkMsg
Flags
float2
floatcomplex
FloatVector
FmmSerialCoordMsg
FmmSerialForceMsg
four_body_consts
FullAtom
gather_t
GBISCoordMsg
GBISForceMsg
GBISInput
GBISInput< 1 >
GBISInput< 2 >
GBISInput< 3 >
GBISParam
GBISParam< 1 >
GBISParam< 2 >
GBISParam< 3 >
GBISParamStruct
GBISResults
GBISResults< 1 >
GBISResults< 2 >
GBISResults< 3 >
GenericAngle
GenericAtom
GenericBond
GenericDihedral
GenericMol
GlobalMaster
GlobalMasterEasy
GlobalMasterFreeEnergy
GlobalMasterIMD
GlobalMasterMisc
GlobalMasterServer
GlobalMasterSMD
GlobalMasterSymmetry
GlobalMasterTcl
GlobalMasterTest
GlobalMasterTMD
go_pair
go_val
GridforceFullBaseGrid
GridIndices
GridforceFullMainGrid
GridforceFullSubGrid
GridforceGrid
GridforceLiteGrid
GridMsg
GroGaussPair
GroLJPair
gromacsPair
GromacsPairElem
GromacsPairValue
GromacsTopFile
GroupInitMsg
HashPool
HashPoolAdaptorT
HashReal
HashString
heapIterator
heapRecord
HomePatch
checkpoint_t
RattleList
HomePatchElem
HydroBasedMsg
HydrogenGroupID
idIndxStr
ijpair
ijpair_sortop_bit_reversed
IMDEnergies
IMDheader
IMDOutput
improper
improper_params
ImproperElem
ImproperValue
indexed_nbthole_pair
indexed_table_pair
indexed_vdw_pair
InfoRecord
infostream
InitDeviceMsg
InitDeviceMsg2
InputAtom
Int2
Int3
InterpParams_t
intpair
IRSet
Iterator
LargeIRSet
Lattice
LCPOAtom
LCPONeighborList
LdbCoordinator
LdbMigrateMsg
listNode
LJTable
TableEntry
LocalID
LocalLBInfoMsg
LocalPmeInfo
LocalWorkMsg
lphost
LSSDataStr
lssDistSort
LSSSubsDat
main
MathArray
Matrix4	4x4 matrix class with numerous operators, conversions, etc
Matrix4Symmetry
Matrix4TMD
maxHeap
Measure
meMMQMGrp
memusageinit
MGridforceParams
MGridforceParamsList
MigrateAtomsCombinedMsg
MigrateAtomsMsg
MigrationInfo
minHeap
minpoint
MIStream
MoaData
Molecule
MolInfoMsg
MolInst
MOStream
MoveAllByMsg
MoveAtomMsg
MoveInputAtomsMsg
MovePatch
MovePatchAtomsMsg
MovePatchesMsg
MsmBlock
MsmBlockKernel
MsmBlockMap
MsmBlockProxyMsg
MsmC1HermiteBlock
MsmC1HermiteBlockProxyMsg
MsmC1HermiteGridCutoff
MsmC1HermiteGridCutoffProxyMsg
MsmC1HermiteGridCutoffSetupMsg
MsmGridCutoff
MsmGridCutoffInitMsg
MsmGridCutoffKernel
MsmGridCutoffMap
MsmGridCutoffProxyMsg
MsmGridCutoffSetupMsg
MsmInitMsg
MsmProfiler
MsmSerialCoordMsg
MsmSerialForceMsg
MsmTimer
NamdCentLB
NamdDummyLB
NamdHybridLB
NamdProfileEvent
NamdState
nbthole_pair_params
nbthole_pair_value
netint	Structure used to perform byte swapping operations
NL_Msm_t
Node
NodePmeInfo
NodePmeMgr
NodeProxyMgr
nodesort
nonbonded
NonbondedCUDASkipMsg
NonbondedCUDASlaveMsg
NonbondedExclValue
NonbondedMICSkipMsg
NonbondedMICSlaveMsg
NumDevicesMsg
ObjectArena
ofstream_namd
Output
OutputAtomRecord
floatVals
integerVals
shortVals
OwnerBox
Pairlists
PairTable
PAL
ParallelIOMgr
Parameters
parm
ParseOptions
DataElement
Patch
patch_sortop_curve_a
patch_sortop_curve_b
patch_sortop_curve_c
patchDataStrc
PatchElem
PatchInfo
patchInfo
PatchMap
PatchMapMsg
PatchMgr
PatchPairRecord
PatchProxyListMsg
PDB
PDBAtom
PDBAtomRecord
PDBData
PDBHetatm
PDBUnknown
pe_sortop_bit_reversed
pe_sortop_coord_x
pe_sortop_coord_y
pid_sortop_reverse_priority
PluginIOMgr
PmeAckMsg
PmeAtomFiler
PmeAtomMsg
PmeAtomPencilMsg
PmeAtomStorage
PmeBlockMsg
PmeDoneMsg
PmeEvirMsg
PmeForceMsg
PmeForcePencilMsg
PmeGrid
PmeGridMsg
PmeKSpace
PmeKSpaceCompute
PmeLaunchMsg
PmeParticle
PmePencil
PmePencilInitMsg
PmePencilInitMsgData
PmePencilMap
PmePencilX
PmePencilXMap
PmePencilXY
PmePencilXYMap
PmePencilXYZ
PmePencilXYZMap
PmePencilY
PmePencilZ
PmeRealSpace
PmeRealSpaceCompute
PmeRunMsg
PmeSharedTransMsg
PmeSharedUntransMsg
PmeStartMsg
PmeTransMsg
PmeTranspose
PmeUntransMsg
PmeXPencil
PmeYPencil
PmeZPencil
pntChrgDist
Pointer
position_index
PressureProfileReduction
processorInfo
ProxyCombinedResultMsg
ProxyCombinedResultRawMsg
ProxyDataMsg
ProxyElem
ProxyGBISP1ResultMsg
ProxyGBISP2DataMsg
ProxyGBISP2ResultMsg
ProxyGBISP3DataMsg
ProxyListInfo
ProxyMgr
ProxyNodeAwareSpanningTreeMsg
ProxyPatch
ProxyResultMsg
ProxyResultVarsizeMsg
ProxySpanningTreeMsg
ProxyTree
proxyTreeNode
ProxyUsage
ProxyUsageKey
QMAtomData
QMCoordMsg
QMForce
QMForceMsg
QMGrpCalcMsg
QMGrpResMsg
QMPntChrgMsg
qmSolvData
Random
RattleParam
Rebalancer
pcpair
RecBisection
RecipVirial_t
RecvDeviceMsg
ReductionMgr
ReductionRegisterMsg
ReductionSet
ReductionSetData
ReductionSubmitMsg
RefineOnly
RefineTorusLB
refSelStr
RegisterPatchMsg
RegisterProxyMsg
ReplicaDcdAckMsg
ReplicaDcdDataMsg
ReplicaDcdInitMsg
RequireReduction
ResidueLookupElem
ResizeArray
ResizeArrayIter
ResizeArrayPrimIter
ResizeArrayRaw
Results
ScriptParamMsg
ScriptTcl
seg_resid
Sequencer
SetLatticeMsg
SimParameters
SimpleBroadcastObject
SlaveInitMsg
SortableResizeArray
SortedArray
sortop_base
sortop_bit_reversed
sortop_x
sortop_y
sortop_z
SplitComputesMsg
StreamMessage
StringList
SubmitReduction
Sync
table_pair_params
TaggedMsg
Tensor
thole
TholeElem
TileExcl
TileList
TileListStat
TileListVirialEnergy
TopoManagerWrapper
pe_sortop_topo
TorusLB
Transform
TransposeBatch
TuplePatchElem
TupleSignature
UniqueSet
UniqueSetIter
UniqueSetRaw
UniqueSortedArray
UnregisterProxyMsg
vdw_pair_params
vdw_params
vdw_val
VDWTable
vect
Vector
VirialEnergy
vmdforce
wkf_timer
wkfmsgtimer
WorkDistrib
pe_sortop_compact
pe_sortop_diffuse
WorkIndex
zVector