| __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 | |
| 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 | |
| colvar | A 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_angles | Colvar 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::angle | Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI]) |
| colvar::coordnum | Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]) |
| colvar::cvc | Colvar component (base class); most implementations of utilize one or more or objects to access atoms |
| colvar::dihedPC | Colvar 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::dihedral | Colvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI]) |
| colvar::distance | Colvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*)) |
| colvar::distance_dir | Colvar 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_inv | Colvar 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_xy | Colvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*)) |
| colvar::distance_z | Colvar component: projection of the distance vector along an axis (colvarvalue::type_scalar type, range (-*:*)) |
| colvar::eigenvector | Colvar component: projection of 3N coordinates onto an eigenvector (colvarvalue::type_scalar type, range (-*:*)) |
| colvar::gyration | Colvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*)) |
| colvar::h_bond | Colvar 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::inertia | Colvar component: moment of inertia of an atom group (colvarvalue::type_scalar type, range [0:*)) |
| colvar::inertia_z | Colvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_scalar type, range [0:*)) |
| colvar::orientation | Colvar 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_angle | Colvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [0:PI)) |
| colvar::rmsd | Colvar 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::selfcoordnum | Colvar component: self-coordination number within a group (colvarvalue::type_scalar type, range [0:N*(N-1)/2]) |
| colvar::spin_angle | Colvar component: angle of rotation around a predefined axis (colvarvalue::type_scalar type, range [-PI:PI]) |
| colvar::tilt | Colvar 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_count | Colvar_grid derived class to hold counters in discrete n-dim colvar space |
| colvar_grid_gradient | Class for accumulating the gradient of a scalar function on a grid |
| colvar_grid_scalar | Class for accumulating a scalar function on a grid |
| colvarbias | Collective variable bias, base class |
| colvarbias_abf | ABF bias |
| colvarbias_harmonic | Harmonic restraint, optionally moving towards a target (implementation of ) |
| colvarbias_histogram | Histogram "bias" (does as the name says) |
| colvarbias_meta | Metadynamics bias (implementation of ) |
| colvarbias_meta::hill | A hill for the metadynamics bias |
| colvarmodule | Collective variables module (main class) |
| colvarmodule::atom | Stores numeric id, mass and all mutable data for an atom, mostly used by a |
| colvarmodule::atom_group | Group 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::quaternion | 1-dimensional vector of real numbers with four components and a quaternion algebra |
| colvarmodule::rmatrix | 2-dimensional array of real numbers with three components along each dimension (works with colvarmodule::rvector) |
| colvarmodule::rotation | A rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion) |
| colvarmodule::rvector | 1-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_block | Helper class to read a block of the type "key { ... }" from a stream and store it in a string |
| colvarproxy | Interface class between the collective variables module and the simulation program |
| colvarproxy_namd | Communication between colvars and NAMD (implementation of ) |
| colvarvalue | Value 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 > | |
| Matrix4 | 4x4 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 | |
| netint | Structure 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 | |
