NAMD
|
#include <Molecule.h>
Friends | |
class | ExclElem |
class | BondElem |
class | AngleElem |
class | DihedralElem |
class | ImproperElem |
class | TholeElem |
class | AnisoElem |
class | CrosstermElem |
class | GromacsPairElem |
class | WorkDistrib |
Definition at line 150 of file Molecule.h.
Molecule::Molecule | ( | SimParameters * | simParams, |
Parameters * | param | ||
) |
Definition at line 429 of file Molecule.C.
Molecule::Molecule | ( | SimParameters * | simParams, |
Parameters * | param, | ||
char * | filename, | ||
ConfigList * | cfgList = NULL |
||
) |
Definition at line 442 of file Molecule.C.
References SimParameters::LCPOOn, and SimParameters::useCompressedPsf.
Molecule::Molecule | ( | SimParameters * | simParams, |
Parameters * | param, | ||
molfile_plugin_t * | pIOHdl, | ||
void * | pIOFileHdl, | ||
int | natoms | ||
) |
Definition at line 464 of file Molecule.C.
References SimParameters::LCPOOn, and NAMD_die().
Molecule::Molecule | ( | SimParameters * | , |
Parameters * | , | ||
Ambertoppar * | |||
) |
Molecule::Molecule | ( | SimParameters * | , |
Parameters * | , | ||
const GromacsTopFile * | |||
) |
Molecule::~Molecule | ( | ) |
Definition at line 558 of file Molecule.C.
References atoms, atomSigPool, exclusions, and exclusionsByAtom.
|
inline |
Definition at line 1048 of file Molecule.h.
Referenced by WorkDistrib::createAtomLists(), NamdState::loadStructure(), Sequencer::reloadCharges(), Sequencer::rescaleSoluteCharges(), colvarproxy_namd::update_atom_properties(), and colvarproxy_namd::update_group_properties().
|
inline |
Definition at line 1038 of file Molecule.h.
References atoms.
Referenced by WorkDistrib::createAtomLists(), GlobalMasterEasy::getMass(), GlobalMasterFreeEnergy::getMass(), NamdState::loadStructure(), Tcl_centerOfMass(), Tcl_radiusOfGyration(), colvarproxy_namd::update_atom_properties(), and colvarproxy_namd::update_group_properties().
Bool Molecule::atoms_1to4 | ( | unsigned int | atom1, |
unsigned int | atom2 | ||
) |
Definition at line 1537 of file GoMolecule.C.
References bond::atom1, angle::atom1, dihedral::atom1, bond::atom2, angle::atom2, dihedral::atom2, angle::atom3, dihedral::atom3, dihedral::atom4, DebugM, FALSE, get_angle(), get_angles_for_atom(), get_bond(), get_bonds_for_atom(), get_dihedral(), get_dihedrals_for_atom(), and TRUE.
Referenced by build_go_arrays(), build_go_sigmas(), and build_go_sigmas2().
|
inline |
Definition at line 1058 of file Molecule.h.
References atoms.
Referenced by WorkDistrib::createAtomLists(), and dumpbench().
void Molecule::build_alch_unpert_bond_lists | ( | char * | ) |
Referenced by NamdState::loadStructure().
void Molecule::build_constant_forces | ( | char * | ) |
Referenced by NamdState::loadStructure().
void Molecule::build_constorque_params | ( | StringList * | , |
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_constraint_params | ( | StringList * | , |
StringList * | , | ||
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_exPressure_atoms | ( | StringList * | , |
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_extra_bonds | ( | Parameters * | parameters, |
StringList * | file | ||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_fep_flags | ( | StringList * | , |
StringList * | , | ||
PDB * | , | ||
char * | , | ||
const char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_fixed_atoms | ( | StringList * | , |
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_go_arrays | ( | StringList * | goCoordFile, |
char * | cwd | ||
) |
goSigmas = new Real[numGoAtoms*numGoAtoms]; goWithinCutoff = new bool[numGoAtoms*numGoAtoms]; for (i=0; i<numGoAtoms; i++) { for (j=0; j<numGoAtoms; j++) { goSigmas[i*numGoAtoms + j] = 0.0; goWithinCutoff[i*numGoAtoms + j] = false; } }
Definition at line 950 of file GoMolecule.C.
References PDB::atom(), atomChainTypes, atoms_1to4(), StringList::data, DebugM, endi(), energyNative, energyNonnative, get_go_cutoff(), go_restricted(), goCoordinates, goPDB, goResids, goSigmaIndices, iINFO(), iout, NAMD_die(), NAMD_FILENAME_BUFFER_SIZE, StringList::next, PDB::num_atoms(), numAtoms, numGoAtoms, PDBAtom::residueseq(), PDBAtom::xcoor(), PDBAtom::ycoor(), and PDBAtom::zcoor().
Referenced by NamdState::loadStructure().
void Molecule::build_go_params | ( | StringList * | g | ) |
Definition at line 79 of file GoMolecule.C.
References StringList::data, endi(), iINFO(), iout, NAMD_die(), StringList::next, and read_go_file().
Referenced by NamdState::loadStructure().
void Molecule::build_go_sigmas | ( | StringList * | goCoordFile, |
char * | cwd | ||
) |
Definition at line 577 of file GoMolecule.C.
References PDB::atom(), atomChainTypes, atoms_1to4(), StringList::data, DebugM, endi(), get_go_cutoff(), get_go_exp_a(), get_go_exp_b(), go_restricted(), goPDB, goSigmaIndices, goSigmas, goWithinCutoff, iINFO(), iout, NAMD_die(), NAMD_FILENAME_BUFFER_SIZE, StringList::next, PDB::num_atoms(), numAtoms, and numGoAtoms.
Referenced by NamdState::loadStructure().
void Molecule::build_go_sigmas2 | ( | StringList * | goCoordFile, |
char * | cwd | ||
) |
Definition at line 747 of file GoMolecule.C.
References go_pair::A, ResizeArray< T >::add(), PDB::atom(), atomChainTypes, atoms_1to4(), go_pair::B, ResizeArray< T >::begin(), StringList::data, DebugM, ResizeArray< T >::end(), endi(), get_go_cutoff(), get_go_exp_a(), get_go_exp_b(), go_restricted(), go_pair::goIndxA, go_pair::goIndxB, goIndxLJA, goIndxLJB, goNumLJPair, goPDB, goResidIndices, goSigmaIndices, goSigmaPairA, goSigmaPairB, iINFO(), iout, NAMD_die(), NAMD_FILENAME_BUFFER_SIZE, StringList::next, PDB::num_atoms(), numAtoms, numGoAtoms, numLJPair, pointerToGoBeg, pointerToGoEnd, and sort.
Referenced by NamdState::loadStructure().
void Molecule::build_gridforce_params | ( | StringList * | gridfrcfile, |
StringList * | gridfrccol, | ||
StringList * | gridfrcchrgcol, | ||
StringList * | potfile, | ||
PDB * | initial_pdb, | ||
char * | cwd | ||
) |
Definition at line 6373 of file Molecule.C.
References PDB::atom(), DebugM, endi(), MGridforceParamsList::get_first(), MGridforceParams::gridforceCol, MGridforceParams::gridforceFile, MGridforceParams::gridforceQcol, MGridforceParams::gridforceVfile, iout, iWARN(), SimParameters::mgridforcelist, NAMD_die(), NAMD_FILENAME_BUFFER_SIZE, GridforceGrid::new_grid(), MGridforceParams::next, and PDB::num_atoms().
Referenced by NamdState::loadStructure().
void Molecule::build_gro_pair | ( | ) |
Referenced by NamdState::loadStructure().
void Molecule::build_langevin_params | ( | StringList * | , |
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
void Molecule::build_movdrag_params | ( | StringList * | , |
StringList * | , | ||
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_rotdrag_params | ( | StringList * | , |
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
void Molecule::build_ss_flags | ( | const StringList * | ssfile, |
const StringList * | sscol, | ||
PDB * | initial_pdb, | ||
const char * | cwd | ||
) |
Build the flags needed for solute scaling.
A PDB file is read, indicating which atoms are to be scaled, and an array is maintained marking which are to be included. Each marked atom then has its corresponding van der Waals type number reassigned to enable extending the LJTable with scaled interaction values.
ssfile | config "soluteScalingFile = my.pdb" for PDB filename |
sscol | config "soluteScalingCol = O" for column of PDB ATOM records |
initial_pdb | the initial PDB file |
cwd | current working directory |
Referenced by NamdState::loadStructure().
void Molecule::build_stirred_atoms | ( | StringList * | , |
StringList * | , | ||
PDB * | , | ||
char * | |||
) |
Referenced by NamdState::loadStructure().
int Molecule::checkexcl | ( | int | atom1, |
int | atom2 | ||
) | const |
void Molecule::compute_LJcorrection | ( | ) |
Referenced by NamdState::loadStructure().
Referenced by NamdState::loadStructure().
Definition at line 1547 of file MoleculeQM.C.
References bond::atom1, angle::atom1, dihedral::atom1, improper::atom1, crossterm::atom1, DebugM, endi(), SimParameters::extraBondsOn, iERROR(), iINFO(), iout, NAMD_die(), numAngles, numBonds, numCrossterms, numDihedrals, numImpropers, and numRealBonds.
|
inline |
Definition at line 1034 of file Molecule.h.
Referenced by NamdState::loadStructure().
|
inline |
Definition at line 1030 of file Molecule.h.
Referenced by NamdState::loadStructure().
|
inline |
Definition at line 1105 of file Molecule.h.
|
inline |
Definition at line 1068 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
|
inline |
Definition at line 1147 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
int Molecule::get_atom_from_index_in_residue | ( | const char * | segid, |
int | resid, | ||
int | index | ||
) | const |
Definition at line 158 of file Molecule.C.
References NAMD_die().
Referenced by GlobalMasterEasy::getAtomID(), and GlobalMasterFreeEnergy::getAtomID().
int Molecule::get_atom_from_name | ( | const char * | segid, |
int | resid, | ||
const char * | aname | ||
) | const |
Definition at line 121 of file Molecule.C.
References atomNamePool, and NAMD_die().
Referenced by colvarproxy_namd::check_atom_id(), GlobalMasterEasy::getAtomID(), and GlobalMasterFreeEnergy::getAtomID().
|
inline |
|
inline |
Definition at line 1065 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
|
inline |
Definition at line 1145 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
|
inline |
Definition at line 1023 of file Molecule.h.
Referenced by wrap_coor_int().
|
inline |
Definition at line 1024 of file Molecule.h.
Referenced by wrap_coor_int().
Definition at line 1262 of file Molecule.h.
Referenced by ComputeRestraints::doForce().
|
inline |
Definition at line 1336 of file Molecule.h.
References consTorqueIndexes, and consTorqueParams.
Referenced by ComputeConsTorque::doForce().
|
inline |
Definition at line 1077 of file Molecule.h.
|
inline |
Definition at line 1153 of file Molecule.h.
|
inline |
Definition at line 874 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 870 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 869 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 872 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 868 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 871 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 873 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 1074 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
|
inline |
Definition at line 1149 of file Molecule.h.
Referenced by atoms_1to4(), and dumpbench().
|
inline |
Definition at line 1102 of file Molecule.h.
|
inline |
Definition at line 1173 of file Molecule.h.
Referenced by dumpbench().
|
inline |
Definition at line 1112 of file Molecule.h.
References exclusions.
|
inline |
Definition at line 1155 of file Molecule.h.
References exclusionsByAtom.
|
inline |
Definition at line 1385 of file Molecule.h.
References NAMD_die(), order, and simParams.
Referenced by AngleElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), AnisoElem::computeForce(), and BondElem::computeForce().
|
inline |
Definition at line 1345 of file Molecule.h.
Referenced by CrosstermElem::computeForce(), TholeElem::computeForce(), WorkDistrib::createAtomLists(), and ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
|
inline |
Definition at line 1157 of file Molecule.h.
Referenced by ComputeNonbondedCUDA::build_exclusions().
|
inline |
Definition at line 1601 of file Molecule.h.
References go_val::cutoff, go_array, and MAX_GO_CHAINS.
Referenced by build_go_arrays(), build_go_sigmas(), build_go_sigmas2(), get_go_force(), get_go_force2(), and get_go_force_new().
|
inline |
Definition at line 1610 of file Molecule.h.
References go_val::epsilon, go_array, and MAX_GO_CHAINS.
Referenced by get_go_force(), get_go_force2(), and get_go_force_new().
|
inline |
Definition at line 1604 of file Molecule.h.
References go_val::epsilonRep, go_array, and MAX_GO_CHAINS.
Referenced by get_go_force(), get_go_force2(), and get_go_force_new().
|
inline |
Definition at line 1613 of file Molecule.h.
References go_val::exp_a, go_array, and MAX_GO_CHAINS.
Referenced by build_go_sigmas(), build_go_sigmas2(), get_go_force(), get_go_force2(), and get_go_force_new().
|
inline |
Definition at line 1616 of file Molecule.h.
References go_val::exp_b, go_array, and MAX_GO_CHAINS.
Referenced by build_go_sigmas(), build_go_sigmas2(), get_go_force(), get_go_force2(), and get_go_force_new().
|
inline |
Definition at line 1619 of file Molecule.h.
References go_val::exp_rep, go_array, and MAX_GO_CHAINS.
Referenced by get_go_force(), get_go_force2(), and get_go_force_new().
BigReal Molecule::get_go_force | ( | BigReal | r, |
int | atom1, | ||
int | atom2, | ||
BigReal * | goNative, | ||
BigReal * | goNonnative | ||
) | const |
Definition at line 1260 of file GoMolecule.C.
References atomChainTypes, get_go_cutoff(), get_go_epsilon(), get_go_epsilonRep(), get_go_exp_a(), get_go_exp_b(), get_go_exp_rep(), get_go_sigmaRep(), goForce, goSigmaIndices, goSigmas, goWithinCutoff, and numGoAtoms.
BigReal Molecule::get_go_force2 | ( | BigReal | x, |
BigReal | y, | ||
BigReal | z, | ||
int | atom1, | ||
int | atom2, | ||
BigReal * | goNative, | ||
BigReal * | goNonnative | ||
) | const |
Definition at line 1456 of file GoMolecule.C.
References atomChainTypes, get_go_cutoff(), get_go_epsilon(), get_go_epsilonRep(), get_go_exp_a(), get_go_exp_b(), get_go_exp_rep(), get_go_sigmaRep(), go_restricted(), goIndxLJB, goResidIndices, goSigmaPairA, goSigmaPairB, pointerToGoBeg, pointerToGoEnd, and z.
BigReal Molecule::get_go_force_new | ( | BigReal | r, |
int | atom1, | ||
int | atom2, | ||
BigReal * | goNative, | ||
BigReal * | goNonnative | ||
) | const |
Definition at line 1334 of file GoMolecule.C.
References atomChainTypes, DebugM, get_go_cutoff(), get_go_epsilon(), get_go_epsilonRep(), get_go_exp_a(), get_go_exp_b(), get_go_exp_rep(), get_go_sigmaRep(), go_restricted(), goCoordinates, goForce, goResids, and goSigmaIndices.
|
inline |
Definition at line 1607 of file Molecule.h.
References go_array, MAX_GO_CHAINS, and go_val::sigmaRep.
Referenced by get_go_force(), get_go_force2(), and get_go_force_new().
|
inline |
Definition at line 1276 of file Molecule.h.
References numGridforceGrids.
Referenced by ComputeGridForce::doForce(), colvarproxy_namd::init_volmap(), Node::reloadGridforceGrid(), and Node::updateGridScale().
Definition at line 1270 of file Molecule.h.
Referenced by ComputeGridForce::do_calc().
BigReal Molecule::get_gro_force2 | ( | BigReal | x, |
BigReal | y, | ||
BigReal | z, | ||
int | atom1, | ||
int | atom2, | ||
BigReal * | pairLJEnergy, | ||
BigReal * | pairGaussEnergy | ||
) | const |
Definition at line 1173 of file GoMolecule.C.
References A, gA, giSigma1, giSigma2, gMu1, gMu2, gRepulsive, indxGaussB, indxLJB, pairC12, pairC6, pointerToGaussBeg, pointerToGaussEnd, pointerToLJBeg, pointerToLJEnd, and z.
int Molecule::get_groupSize | ( | int | ) |
|
inline |
Definition at line 1071 of file Molecule.h.
Referenced by dumpbench().
|
inline |
Definition at line 1151 of file Molecule.h.
Referenced by dumpbench().
|
inline |
Definition at line 1081 of file Molecule.h.
|
inline |
Definition at line 1159 of file Molecule.h.
int Molecule::get_mother_atom | ( | int | ) |
Definition at line 1321 of file Molecule.h.
Referenced by Sequencer::addMovDragToPosition().
|
inline |
Definition at line 856 of file Molecule.h.
Referenced by ComputeQM::initialize().
|
inline |
Definition at line 825 of file Molecule.h.
Referenced by ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), ComputePme::doQMWork(), ComputeQM::initialize(), ComputeQMMgr::procQMRes(), HomePatch::qmSwapAtoms(), ComputeQMMgr::recvPartQM(), and ComputeQM::saveResults().
|
inline |
Definition at line 822 of file Molecule.h.
Referenced by ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), ComputePme::doQMWork(), ComputeQM::initialize(), HomePatch::qmSwapAtoms(), and ComputeQM::saveResults().
|
inline |
Definition at line 823 of file Molecule.h.
Referenced by ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), ComputePme::doQMWork(), ComputeQM::initialize(), HomePatch::qmSwapAtoms(), and ComputeQM::saveResults().
|
inline |
Definition at line 819 of file Molecule.h.
Referenced by ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), ComputePme::doQMWork(), ComputeQM::initialize(), HomePatch::qmSwapAtoms(), and ComputeQM::saveResults().
|
inline |
Definition at line 820 of file Molecule.h.
|
inline |
Definition at line 867 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 865 of file Molecule.h.
Referenced by ComputeQM::initialize().
|
inline |
Definition at line 864 of file Molecule.h.
Referenced by ComputeQM::initialize().
|
inline |
Definition at line 834 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
|
inline |
Definition at line 839 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
|
inline |
Definition at line 826 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
|
inline |
Definition at line 837 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
|
inline |
Definition at line 830 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 829 of file Molecule.h.
Referenced by ComputeQM::initialize(), and ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 831 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 835 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
|
inline |
Definition at line 828 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
|
inline |
Definition at line 847 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 845 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 846 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 849 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 851 of file Molecule.h.
|
inline |
Definition at line 850 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 848 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 844 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 858 of file Molecule.h.
Referenced by ComputeQM::initialize().
|
inline |
Definition at line 857 of file Molecule.h.
Referenced by ComputeQM::initialize(), and ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 859 of file Molecule.h.
Referenced by ComputeQM::initialize().
|
inline |
Definition at line 836 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
|
inline |
Definition at line 838 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
|
inline |
Definition at line 841 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
|
inline |
Definition at line 842 of file Molecule.h.
Referenced by ComputeQMMgr::recvPntChrg().
|
inline |
Definition at line 852 of file Molecule.h.
|
inline |
Definition at line 833 of file Molecule.h.
|
inline |
Definition at line 827 of file Molecule.h.
Referenced by ComputeQM::initialize(), ComputeQMMgr::recvPartQM(), and ComputeQM::saveResults().
|
inline |
Definition at line 861 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 854 of file Molecule.h.
Referenced by ComputeQMMgr::recvPartQM().
|
inline |
Definition at line 863 of file Molecule.h.
Referenced by ComputeQM::initialize().
int Molecule::get_residue_size | ( | const char * | segid, |
int | resid | ||
) | const |
Definition at line 144 of file Molecule.C.
References NAMD_die().
Referenced by GlobalMasterEasy::getNumAtoms(), GlobalMasterFreeEnergy::getNumAtoms(), and prepare_qm().
Definition at line 1327 of file Molecule.h.
Referenced by Sequencer::addRotDragToPosition().
|
inline |
Definition at line 1351 of file Molecule.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), and Sequencer::rescaleSoluteCharges().
Definition at line 1302 of file Molecule.h.
|
inline |
Definition at line 1314 of file Molecule.h.
Referenced by ComputeStir::doForce().
|
inline |
Definition at line 1108 of file Molecule.h.
|
inline |
|
inline |
|
inline |
Definition at line 1094 of file Molecule.h.
Referenced by buildCrosstermData().
|
inline |
Definition at line 1093 of file Molecule.h.
Referenced by buildDihedralData().
|
inline |
Definition at line 1107 of file Molecule.h.
|
inline |
Definition at line 1092 of file Molecule.h.
Referenced by buildImproperData().
|
inline |
Definition at line 1098 of file Molecule.h.
|
inline |
|
inline |
|
inline |
Definition at line 490 of file Molecule.h.
References atoms.
Referenced by buildAtomData(), WorkDistrib::createAtomLists(), and outputCompressedFile().
|
inline |
Definition at line 494 of file Molecule.h.
Referenced by buildAtomData().
|
inline |
Definition at line 1032 of file Molecule.h.
Referenced by NamdState::loadStructure(), and outputCompressedFile().
Referenced by Controller::printEnergies().
|
inline |
Definition at line 478 of file Molecule.h.
Referenced by HomePatch::setLcpoType().
|
inline |
Definition at line 1028 of file Molecule.h.
Referenced by NamdState::loadStructure(), and outputCompressedFile().
Referenced by Controller::calcPressure().
Bool Molecule::go_restricted | ( | int | chain1, |
int | chain2, | ||
int | rDiff | ||
) |
Definition at line 525 of file GoMolecule.C.
References FALSE, go_array, MAX_GO_CHAINS, MAX_RESTRICTIONS, and TRUE.
Referenced by build_go_arrays(), build_go_sigmas(), build_go_sigmas2(), get_go_force2(), and get_go_force_new().
void Molecule::goInit | ( | ) |
Definition at line 54 of file GoMolecule.C.
References atomChainTypes, energyNative, energyNonnative, goCoordinates, goPDB, goResids, goSigmaIndices, goSigmas, goWithinCutoff, and numGoAtoms.
void Molecule::initialize | ( | ) |
|
inline |
|
inline |
Definition at line 1197 of file Molecule.h.
References FALSE, and numConstraints.
Referenced by ComputeRestraints::doForce().
|
inline |
Definition at line 1447 of file Molecule.h.
References numExPressureAtoms.
Referenced by Sequencer::langevinPiston().
|
inline |
Definition at line 1407 of file Molecule.h.
References numFixedAtoms.
Referenced by WorkDistrib::createAtomLists().
|
inline |
Definition at line 1181 of file Molecule.h.
References FALSE, and numGridforceGrids.
Referenced by ComputeGridForce::do_calc().
|
inline |
Definition at line 1214 of file Molecule.h.
References FALSE, and numMovDrag.
Referenced by Sequencer::addMovDragToPosition().
|
inline |
Definition at line 1230 of file Molecule.h.
References FALSE, and numRotDrag.
Referenced by Sequencer::addRotDragToPosition().
|
inline |
Definition at line 1428 of file Molecule.h.
References FALSE, and numStirredAtoms.
Referenced by ComputeStir::doForce().
Bool Molecule::is_drude | ( | int | ) |
|
inline |
Bool Molecule::is_hydrogen | ( | int | ) |
Bool Molecule::is_hydrogenGroupParent | ( | int | ) |
Bool Molecule::is_lp | ( | int | ) |
Bool Molecule::is_oxygen | ( | int | ) |
Bool Molecule::is_water | ( | int | ) |
Referenced by outputCompressedFile(), and wrap_coor_int().
|
inline |
Definition at line 1296 of file Molecule.h.
Referenced by WorkDistrib::createAtomLists().
|
inline |
Definition at line 523 of file Molecule.h.
References num_fixed_atoms(), numAtoms, numConstraints, numFepInitial, numFixedRigidBonds, numLonepairs, numRigidBonds, simParams, and WAT_TIP4.
Referenced by Controller::Controller(), NamdState::loadStructure(), and Controller::receivePressure().
|
inline |
Definition at line 497 of file Molecule.h.
References numFixedAtoms, and simParams.
Referenced by num_deg_freedom(), num_fixed_groups(), num_group_deg_freedom(), and Controller::receivePressure().
|
inline |
Definition at line 503 of file Molecule.h.
References num_fixed_atoms(), and numFixedGroups.
Referenced by num_group_deg_freedom(), and Controller::receivePressure().
|
inline |
Definition at line 510 of file Molecule.h.
References num_fixed_atoms(), num_fixed_groups(), numConstraints, numHydrogenGroups, and simParams.
Referenced by Controller::receivePressure().
void Molecule::prepare_qm | ( | const char * | pdbFileName, |
Parameters * | params, | ||
ConfigList * | cfgList | ||
) |
Prepares Live Solvent Selection
Data gathering from PDB to find QM atom and bond info
Multiplicity of each QM group
Charge of each QM group
Populate arrays that are used throughout the the calculations.
Overides Link Atom element with user selection.
Bond Schemes. Prepares for treatment of QM-MM bonds in ComputeQM.C
Live Solvent Selection
Custom Point Charge selection
Topology preparation
Definition at line 109 of file MoleculeQM.C.
References Parameters::assign_vdw_index(), qmSolvData::atmIDs, PDB::atom(), bond::atom1, bond::atom2, ResizeArray< T >::begin(), bond::bond_type, atom_constants::charge, charge, StringList::data, DebugM, PDBAtom::element(), ResizeArray< T >::end(), endi(), SimParameters::extraBondsOn, SortedArray< Type >::find(), ConfigList::find(), SimParameters::fixedAtomsOn, get_residue_size(), ObjectArena< Type >::getNewArray(), iERROR(), iINFO(), SortedArray< Type >::insert(), iout, iWARN(), ResidueLookupElem::lookup(), atom_constants::mass, NAMD_blank_string(), NAMD_die(), NAMD_read_line(), StringList::next, PDB::num_atoms(), numAtoms, numBonds, numRealBonds, PDBAtom::occupancy(), SimParameters::PMEOn, SimParameters::qmBondDist, SimParameters::qmBondOn, SimParameters::qmBondScheme, SimParameters::qmChrgFromPSF, SimParameters::qmColumn, SimParameters::qmCSMD, SimParameters::qmCustomPCSel, SimParameters::qmElecEmbed, SimParameters::qmFormat, QMFormatMOPAC, QMFormatORCA, SimParameters::qmLSSFreq, SimParameters::qmLSSMode, QMLSSMODECOM, QMLSSMODEDIST, SimParameters::qmLSSOn, SimParameters::qmLSSResname, SimParameters::qmMOPACAddConfigChrg, SimParameters::qmNoPC, SimParameters::qmPCSelFreq, QMSCHEMECS, QMSCHEMERCD, QMSCHEMEZ1, QMSCHEMEZ2, QMSCHEMEZ3, SimParameters::qmVDW, PDBAtom::residuename(), PDBAtom::residueseq(), PDBAtom::segmentname(), ResizeArray< T >::size(), split(), SimParameters::stepsPerCycle, and PDBAtom::temperaturefactor().
Referenced by NamdState::loadStructure().