Index

_

__init__() (pygromos.analysis.error_estimate.error_estimator method) (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio method) (pygromos.analysis.free_energy_calculation.threeStateZwanzig method) (pygromos.analysis.free_energy_calculation.zwanzigEquation method) (pygromos.data.ff.atomType.AtomType method) (pygromos.files.blocks.coord_blocks.atomP method) (pygromos.files.blocks.coord_blocks.GENBOX method) (pygromos.files.blocks.coord_blocks.LATTICESHIFTS method) (pygromos.files.blocks.coord_blocks.PERTDATA method) (pygromos.files.blocks.coord_blocks.REFPOSITION method) (pygromos.files.blocks.imd_blocks.CONSTRAINT method) (pygromos.files.blocks.imd_blocks.DISTANCERES method) (pygromos.files.blocks.imd_blocks.FORCE method) (pygromos.files.blocks.imd_blocks.INITIALISE method) (pygromos.files.blocks.imd_blocks.PAIRLIST method) (pygromos.files.blocks.imd_blocks.PRECALCLAM method) (pygromos.files.blocks.imd_blocks.REPLICA_EDS method) (pygromos.files.blocks.imd_blocks.WRITETRAJ method) (pygromos.files.blocks.miscBlocks.ATOMNAMELIB method) (pygromos.files.blocks.miscBlocks.RESIDUENAMELIB method) (pygromos.files.blocks.pertubation_blocks.MPERTATOM method) (pygromos.files.blocks.qmmm_blocks.qmzone_field method) (pygromos.files.blocks.replica_exchange_blocks.replica_stat method) (pygromos.files.blocks.topology_blocks.angle_type method) (pygromos.files.blocks.topology_blocks.atom_pair_distanceRes method) (pygromos.files.blocks.topology_blocks.BOND method) (pygromos.files.blocks.topology_blocks.bond_type method) (pygromos.files.blocks.topology_blocks.BONDANGLE method) (pygromos.files.blocks.topology_blocks.bondangle_type method) (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPE method) (pygromos.files.blocks.topology_blocks.bondanglebendtype_type method) (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPECODE method) (pygromos.files.blocks.topology_blocks.BONDANGLEH method) (pygromos.files.blocks.topology_blocks.BONDH method) (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPE method) (pygromos.files.blocks.topology_blocks.bondstretchtype_type method) (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPECODE method) (pygromos.files.blocks.topology_blocks.constraint_type method) (pygromos.files.blocks.topology_blocks.CROSSDIHEDRAL method) (pygromos.files.blocks.topology_blocks.CROSSDIHEDRALH method) (pygromos.files.blocks.topology_blocks.crossgihedral_type method) (pygromos.files.blocks.topology_blocks.crossgihedralh_type method) (pygromos.files.blocks.topology_blocks.DIHEDRAL method) (pygromos.files.blocks.topology_blocks.dihedral_type method) (pygromos.files.blocks.topology_blocks.DIHEDRALH method) (pygromos.files.blocks.topology_blocks.dihedralh_type method) (pygromos.files.blocks.topology_blocks.DISTANCERESSPEC method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRAL method) (pygromos.files.blocks.topology_blocks.impdihedral_type method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALH method) (pygromos.files.blocks.topology_blocks.impdihedralh_type method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPE method) (pygromos.files.blocks.topology_blocks.impdihedraltype_type method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPECODE method) (pygromos.files.blocks.topology_blocks.improper_dihedral_type method) (pygromos.files.blocks.topology_blocks.ljexception_type method) (pygromos.files.blocks.topology_blocks.LJEXCEPTIONS method) (pygromos.files.blocks.topology_blocks.LJPARAMETERS method) (pygromos.files.blocks.topology_blocks.ljparameters_type method) (pygromos.files.blocks.topology_blocks.MIXEDATOMLJPAIR method) (pygromos.files.blocks.topology_blocks.SCALEDINTERACTIONS method) (pygromos.files.blocks.topology_blocks.single_atom_lj_pair_type method) (pygromos.files.blocks.topology_blocks.SINGLEATOMLJPAIR method) (pygromos.files.blocks.topology_blocks.soluteatom_type method) (pygromos.files.blocks.topology_blocks.SOLVENTATOM method) (pygromos.files.blocks.topology_blocks.solventatom_type method) (pygromos.files.blocks.topology_blocks.SOLVENTCONSTR method) (pygromos.files.blocks.topology_blocks.solventconstr_type method) (pygromos.files.blocks.topology_blocks.SPECATOMLJPAIR method) (pygromos.files.blocks.topology_blocks.special_atom_lj_pair_type method) (pygromos.files.blocks.topology_blocks.top_bond_type method) (pygromos.files.blocks.topology_blocks.top_dihedral_type method) (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPE method) (pygromos.files.blocks.topology_blocks.torsdihedraltype_type method) (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPECODE method) (pygromos.files.forcefield.amber.amberff.amber2gromos method) (pygromos.files.gromos_system.gromos_system.Gromos_System method) (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.repdat.Repdat method) (pygromos.files.otherfiles.residue_library.residue_library method) (pygromos.files.trajectory.tre.Tre method) (pygromos.gromos.gromosPP._gromosPPbase method) (pygromos.gromos.gromosXX._GromosXX method) (pygromos.simulations.approaches.hvap_calculation.hvap_calculation.Hvap_calculation method) (pygromos.utils.compiledProgram._compiled_program method)

_add_top() (pygromos.files.topology.top.Top method) _caculate_transition_traces() (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.repdat.Repdat method) _calc_bar() (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio method) _calc_bar_mpmath() (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio method) _calculate_efficient() (pygromos.analysis.free_energy_calculation.zwanzigEquation method) _calculate_implementation_bruteForce() (pygromos.analysis.free_energy_calculation.zwanzigEquation method) _calculate_implementation_useZwanzig() (pygromos.analysis.free_energy_calculation.threeStateZwanzig method) _calculate_meanEfficient() (pygromos.analysis.free_energy_calculation.zwanzigEquation method) _calculate_mpmath() (pygromos.analysis.free_energy_calculation.zwanzigEquation method) _calculate_ndowns_nups_for_each_state() (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.repdat.Repdat method) _calculate_optimize() (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio method) _calculate_replica_roundtrips() (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.repdat.Repdat method) _check_all_binaries() (pygromos.utils.compiledProgram._compiled_program method) _check_binaries_decorator() (pygromos.utils.compiledProgram._compiled_program method) _check_binary() (pygromos.utils.compiledProgram._compiled_program method) _check_binary_dir() (pygromos.utils.compiledProgram._compiled_program method) _clean_replica_round_trips() (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.repdat.Repdat method) _compiled_program (class in pygromos.utils.compiledProgram) _compiled_program__wrap_programms_with_binary_checks() (pygromos.utils.compiledProgram._compiled_program method) _configure_gromosPP_autotools() (in module pygromos.gromos.compile_gromos) _configure_gromosXX_autotools() (in module pygromos.gromos.compile_gromos) _get_numberOfForceGroupsFromNonbondeds() (pygromos.files.trajectory.tre.Tre method) _gromosPPbase (class in pygromos.gromos.gromosPP) _GromosXX (class in pygromos.gromos.gromosXX) _health_check() (pygromos.files.qmmm.qmmm.QMMM method) _inline_dict() (in module pygromos.utils.utils) _make_clean() (in module pygromos.gromos.compile_gromos) _make_compile() (in module pygromos.gromos.compile_gromos) _set_data() (pygromos.files.trajectory.tre.Tre method) _thread_worker_cat_trc() (in module pygromos.simulations.hpc_queuing.job_scheduling.file_management)

A

adapt_energy_groups() (pygromos.files.blocks.imd_blocks.FORCE method) adapt_imd() (pygromos.files.gromos_system.gromos_system.Gromos_System method) adapt_multibath() (pygromos.files.blocks.imd_blocks.MULTIBATH method) add_empty_box() (pygromos.files.coord.cnf.Cnf method) add_hydrogens() (pygromos.gromos.gromosPP._gromosPPbase method) add_new_angle() (pygromos.files.topology.top.Top method) add_new_atom() (pygromos.files.topology.top.Top method) add_new_atomtype() (pygromos.files.topology.top.Top method) add_new_bond() (pygromos.files.topology.top.Top method) add_new_CONSTRAINT() (pygromos.files.topology.top.Top method) add_new_crossdihedral() (pygromos.files.topology.top.Top method) add_new_impdihedral() (pygromos.files.topology.top.Top method) add_new_impdihedral_type() (pygromos.files.topology.top.Top method) add_new_LJparameter() (pygromos.files.topology.top.Top method) add_new_PRESSUREGROUPS() (pygromos.files.topology.top.Top method) add_new_resname() (pygromos.files.topology.top.Top method) add_new_soluteatom() (pygromos.files.topology.top.Top method) add_new_SOLUTEMOLECULES() (pygromos.files.topology.top.Top method) add_new_TEMPERATUREGROUPS() (pygromos.files.topology.top.Top method) add_new_torsiondihedral() (pygromos.files.topology.top.Top method) add_residue_positions() (pygromos.files.coord.cnf.Cnf method) add_state_atoms() (pygromos.files.blocks.pertubation_blocks.MPERTATOM method) (pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM method) (pygromos.files.blocks.topology_blocks.PERTATOMPARAM method) addAtomType() (in module pygromos.data.ff.addAtomType) added_property (pygromos.files.otherfiles.new_repdat.Repdat attribute) addToMatrix() (pygromos.data.ff.atomType.AtomType method) ALGORITHM (pygromos.files.blocks.imd_blocks.MULTIBATH attribute) (pygromos.files.blocks.imd_blocks.PAIRLIST attribute) ALI (pygromos.files.blocks.imd_blocks.LAMBDA attribute) all_blocks_class (class in pygromos.files.blocks) all_file_paths (pygromos.files.gromos_system.gromos_system.Gromos_System property) all_files (pygromos.files.gromos_system.gromos_system.Gromos_System property) all_res_names (pygromos.files.topology.mtb.Mtb attribute) ALPHC (pygromos.files.blocks.imd_blocks.PERTURBATION attribute) ALPHLJ (pygromos.files.blocks.imd_blocks.PERTURBATION attribute) AMBER (class in pygromos.files.blocks.imd_blocks) Amber (pygromos.files.blocks.imd_blocks.AMBER attribute) amber2gromos (class in pygromos.files.forcefield.amber.amberff) amber2gromos() (pygromos.files.forcefield.amber.amberff.amber2gromos method) (pygromos.gromos.gromosPP._gromosPPbase method)

AmberFF (class in pygromos.files.forcefield.amber.amberff) AMBSCAL (pygromos.files.blocks.imd_blocks.AMBER attribute) amino_acid (class in pygromos.utils.amino_acids) angle_type (class in pygromos.files.blocks.topology_blocks) angles (pygromos.files.blocks.coord_blocks.GENBOX property) ANGLES (pygromos.files.blocks.imd_blocks.FORCE attribute) angles (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE attribute) antechamber() (pygromos.files.forcefield.amber.amberff.amber2gromos method) APPAK (pygromos.files.blocks.imd_blocks.NONBONDED attribute) append() (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.repdat.Repdat method) ASHAPE (pygromos.files.blocks.imd_blocks.NONBONDED attribute) atom_eds_pertubation_state (class in pygromos.files.blocks.pertubation_blocks) atom_lam_pertubation_state (class in pygromos.files.blocks.pertubation_blocks) (class in pygromos.files.blocks.topology_blocks) atom_lam_pertubation_state_angle (class in pygromos.files.blocks.pertubation_blocks) atom_lam_pertubation_state_bond (class in pygromos.files.blocks.pertubation_blocks) atom_lam_pertubation_state_dihedral (class in pygromos.files.blocks.pertubation_blocks) atom_mass_type (class in pygromos.files.blocks.pertubation_blocks) (class in pygromos.files.blocks.topology_blocks) atom_pair_distanceRes (class in pygromos.files.blocks.topology_blocks) atom_ref_pos_block (pygromos.files.coord.cnf.Cnf attribute) ATOMNAMELIB (class in pygromos.files.blocks.miscBlocks) (pygromos.files.otherfiles.residue_library.residue_library attribute) atomP (class in pygromos.files.blocks.coord_blocks) atoms (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLVENT attribute) atomSI (class in pygromos.files.blocks.coord_blocks) atomSliceParser() (pygromos.gromos.gromosBashSyntaxParser.gromosBashSyntaxParser static method) AtomType (class in pygromos.data.ff.atomType) ATOMTYPENAME (class in pygromos.files.blocks.topology_blocks) atomV (class in pygromos.files.blocks.coord_blocks) auto_convert() (pygromos.files.gromos_system.gromos_system.Gromos_System method) auto_import_ff() (pygromos.files.forcefield.amber.amberff.AmberFF method) (pygromos.files.forcefield.gromos.gromosff.GromosFF method) (pygromos.files.forcefield.openff.openff.OpenFF method) (pygromos.files.forcefield.serenityff.serenityff.SerenityFF method) AVERAGE_NOE (pygromos.files.otherfiles.noe_output.NOE attribute)

B

bar (class in pygromos.analysis.free_energy_calculation) baths (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) bennetAcceptanceRatio (class in pygromos.analysis.free_energy_calculation) beta (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) bin (pygromos.utils.compiledProgram._compiled_program property) BLI (pygromos.files.blocks.imd_blocks.LAMBDA attribute) block_to_string() (pygromos.files.blocks.coord_blocks.GENBOX method) (pygromos.files.blocks.coord_blocks.STOCHINT method) (pygromos.files.blocks.imd_blocks.MULTIBATH method) (pygromos.files.blocks.miscBlocks.ATOMNAMELIB method) (pygromos.files.blocks.miscBlocks.RESIDUENAMELIB method) (pygromos.files.blocks.mtb_blocks.LINKEXCLUSIONS method) (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND method) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE method) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLVENT method) (pygromos.files.blocks.pertubation_blocks.MPERTATOM method) (pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM method) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLE method) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLEH method) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCH method) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCHH method) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIH method) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIHH method) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIH method) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH method) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH.PERTPROPERDIH method) (pygromos.files.blocks.pertubation_blocks.TITLE method) (pygromos.files.blocks.qmmm_blocks.QMUNIT method) (pygromos.files.blocks.qmmm_blocks.QMZONE method) (pygromos.files.blocks.replica_exchange_blocks.repex_system method) (pygromos.files.blocks.topology_blocks.BOND method) (pygromos.files.blocks.topology_blocks.BONDANGLE method) (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPE method) (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPECODE method) (pygromos.files.blocks.topology_blocks.BONDANGLEH method) (pygromos.files.blocks.topology_blocks.BONDH method) (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPE method) (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPECODE method) (pygromos.files.blocks.topology_blocks.CONSTRAINT method) (pygromos.files.blocks.topology_blocks.CROSSDIHEDRAL method) (pygromos.files.blocks.topology_blocks.CROSSDIHEDRALH method) (pygromos.files.blocks.topology_blocks.DIHEDRAL method) (pygromos.files.blocks.topology_blocks.DIHEDRALH method) (pygromos.files.blocks.topology_blocks.DISTANCERESSPEC method) (pygromos.files.blocks.topology_blocks.FORCEFIELD method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRAL method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALH method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPE method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPECODE method) (pygromos.files.blocks.topology_blocks.LJEXCEPTIONS method) (pygromos.files.blocks.topology_blocks.LJPARAMETERS method) (pygromos.files.blocks.topology_blocks.MAKETOPVERSION method) (pygromos.files.blocks.topology_blocks.MASSATOMTYPECODE method) (pygromos.files.blocks.topology_blocks.MIXEDATOMLJPAIR method) (pygromos.files.blocks.topology_blocks.PERTATOMPARAM method) (pygromos.files.blocks.topology_blocks.PHYSICALCONSTANTS method) (pygromos.files.blocks.topology_blocks.SCALEDINTERACTIONS method) (pygromos.files.blocks.topology_blocks.SINGLEATOMLJPAIR method) (pygromos.files.blocks.topology_blocks.SOLUTEATOM method) (pygromos.files.blocks.topology_blocks.SOLVENTATOM method) (pygromos.files.blocks.topology_blocks.SOLVENTCONSTR method) (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPE method) (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPECODE method)

BOND (class in pygromos.files.blocks.topology_blocks) bond_type (class in pygromos.files.blocks.topology_blocks) BONDANGLE (class in pygromos.files.blocks.topology_blocks) bondangle_type (class in pygromos.files.blocks.topology_blocks) BONDANGLEBENDTYPE (class in pygromos.files.blocks.topology_blocks) bondanglebendtype_type (class in pygromos.files.blocks.topology_blocks) BONDANGLEBENDTYPECODE (class in pygromos.files.blocks.topology_blocks) BONDANGLEH (class in pygromos.files.blocks.topology_blocks) bonded (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) BONDH (class in pygromos.files.blocks.topology_blocks) BONDS (pygromos.files.blocks.imd_blocks.FORCE attribute) bonds (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE attribute) BONDSTRETCHTYPE (class in pygromos.files.blocks.topology_blocks) bondstretchtype_type (class in pygromos.files.blocks.topology_blocks) BONDSTRETCHTYPECODE (class in pygromos.files.blocks.topology_blocks) BOUNDCOND (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) build_box() (pygromos.gromos.gromosPP._gromosPPbase method)

C

C (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) calc_hvap() (pygromos.simulations.approaches.hvap_calculation.hvap_calculation.Hvap_calculation method) calculate() (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio method) (pygromos.analysis.free_energy_calculation.threeStateZwanzig method) (pygromos.analysis.free_energy_calculation.zwanzigEquation method) calculate_distance() (in module pygromos.analysis.coordinate_analysis) calculate_error_estimate() (pygromos.analysis.error_estimate.error_estimator method) calculate_rmsd() (pygromos.analysis.error_estimate.error_estimator method) CDIR (pygromos.files.blocks.imd_blocks.DISTANCERES attribute) center_of_geometry() (pygromos.files.coord.cnf.Cnf method) CFRIC (pygromos.files.blocks.imd_blocks.STOCHDYN attribute) chain_submission() (in module pygromos.simulations.hpc_queuing.job_scheduling.schedulers.scheduler_functions) check() (in module pygromos.data.ff.addAtomType) check_ATOM_columns() (in module pygromos.utils.pdb) check_path_dependencies() (in module pygromos.utils.bash) check_top() (in module pygromos.files.topology.top) class_name (pygromos.tests.test_files.test_trajectory.test_trc attribute) (pygromos.tests.test_files.test_trajectory.test_tre attribute) (pygromos.tests.test_files.test_trajectory.test_trg attribute) (pygromos.tests.test_files.test_trajectory.traj_standard_tests attribute) class_type (pygromos.tests.test_files.test_cnf_funcs.test_cnf attribute) (pygromos.tests.test_files.test_disres.test_disres attribute) (pygromos.tests.test_files.test_disres_file.test_disres attribute) (pygromos.tests.test_files.test_gromosSystem.test_gromos_system attribute) (pygromos.tests.test_files.test_imd.test_imd attribute) (pygromos.tests.test_files.test_mtb.test_mtb attribute) (pygromos.tests.test_files.test_ptp.test_ptp attribute) (pygromos.tests.test_files.test_qmmm.test_qmmm attribute) (pygromos.tests.test_files.test_qmmm.test_qmmm_imd attribute) (pygromos.tests.test_files.test_repdat.test_repdat attribute) (pygromos.tests.test_files.test_resnlib.test_resnlib attribute) (pygromos.tests.test_files.test_top.test_top attribute) (pygromos.tests.test_files.test_top.test_top_simple attribute) clean (pygromos.files.forcefield.amber.amberff.AmberFF attribute) clean_file_runs() (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.repdat.Repdat method) clean_posiResNums() (pygromos.files.coord.cnf.Cnf method) cleanup() (pygromos.files.forcefield.amber.amberff.amber2gromos method) CLI (pygromos.files.blocks.imd_blocks.LAMBDA attribute) Cnf (class in pygromos.files.coord.cnf) cnf (pygromos.files.gromos_system.gromos_system.Gromos_System property) cog() (pygromos.gromos.gromosPP._gromosPPbase method) com_top() (in module pygromos.gromos.pyGromosPP.com_top) (pygromos.gromos.gromosPP._gromosPPbase method) COMBATH (pygromos.files.blocks.imd_blocks.MULTIBATH attribute) combine_topologies() (in module pygromos.files.topology.top) command (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property) command_exists() (in module pygromos.utils.bash) comment (pygromos.files.blocks.coord_blocks.GENBOX attribute) (pygromos.files.blocks.coord_blocks.LATTICESHIFTS attribute) (pygromos.files.blocks.coord_blocks.POSITION attribute) (pygromos.files.blocks.coord_blocks.POSRESSPEC attribute) (pygromos.files.blocks.coord_blocks.REFPOSITION attribute) (pygromos.files.blocks.coord_blocks.STOCHINT attribute) (pygromos.files.blocks.coord_blocks.VELOCITY attribute) (pygromos.files.blocks.mtb_blocks.mtb_blocks attribute) (pygromos.files.blocks.pertubation_blocks.MPERTATOM attribute) (pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM attribute) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLE attribute) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLEH attribute) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCH attribute) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCHH attribute) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIH attribute) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIHH attribute) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIH attribute) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH attribute) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH.PERTPROPERDIH attribute) (pygromos.files.blocks.replica_exchange_blocks.repex_system attribute) (pygromos.files.blocks.topology_blocks.DISTANCERESSPEC attribute) (pygromos.files.blocks.topology_blocks.PERTATOMPARAM attribute) (pygromos.files.blocks.topology_blocks.SCALEDINTERACTIONS attribute) COMP (pygromos.files.blocks.imd_blocks.PRESSURESCALE attribute)

compress_files() (in module pygromos.simulations.hpc_queuing.job_scheduling.file_management) compress_gzip() (in module pygromos.utils.bash) compress_tar() (in module pygromos.utils.bash) COMTRANSROT (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) concatenate_text_files() (in module pygromos.utils.bash) consecutivley_renumber() (in module pygromos.utils.pdb) constants (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) (pygromos.analysis.free_energy_calculation.zwanzig attribute) (pygromos.analysis.free_energy_calculation.zwanzigEquation attribute) CONSTRAINT (class in pygromos.files.blocks.imd_blocks) (class in pygromos.files.blocks.topology_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) constraint_type (class in pygromos.files.blocks.topology_blocks) constraints (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLVENT attribute) CONT (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) (pygromos.files.blocks.imd_blocks.REPLICA attribute) (pygromos.files.blocks.imd_blocks.REPLICA_EDS attribute) content (pygromos.files.blocks.coord_blocks.GENBOX attribute) (pygromos.files.blocks.coord_blocks.PERTDATA attribute) (pygromos.files.blocks.mtb_blocks.mtb_blocks attribute) (pygromos.files.blocks.pertubation_blocks.MPERTATOM attribute) (pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM attribute) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLE attribute) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLEH attribute) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCH attribute) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCHH attribute) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIH attribute) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIHH attribute) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIH attribute) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH attribute) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH.PERTPROPERDIH attribute) (pygromos.files.blocks.pertubation_blocks.TITLE attribute) (pygromos.files.blocks.replica_exchange_blocks.repex_system attribute) (pygromos.files.blocks.topology_blocks.DISTANCERESSPEC attribute) (pygromos.files.blocks.topology_blocks.PERTATOMPARAM attribute) (pygromos.files.blocks.topology_blocks.SCALEDINTERACTIONS attribute) (pygromos.files.otherfiles.noe_output.JVAL attribute) convergence_radius (pygromos.analysis.free_energy_calculation.bar attribute) (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) convert() (pygromos.files.forcefield.openff.openff.OpenFF method) convert_other_stuff() (pygromos.files.forcefield.openff.openff.OpenFF method) convertAngles() (pygromos.files.forcefield.openff.openff.OpenFF method) convertBonds() (pygromos.files.forcefield.openff.openff.OpenFF method) convertImproper() (pygromos.files.forcefield.openff.openff.OpenFF method) convertResname() (pygromos.files.forcefield.openff.openff.OpenFF method) convertTosions() (pygromos.files.forcefield.openff.openff.OpenFF method) convertVdW() (pygromos.files.forcefield.openff.openff.OpenFF method) copy() (pygromos.files.gromos_system.gromos_system.Gromos_System method) copy_file() (in module pygromos.utils.bash) count_residue_atoms() (pygromos.files.coord.cnf.Cnf method) count_state_per_position (pygromos.files.otherfiles.new_repdat.Repdat attribute) (pygromos.files.otherfiles.repdat.Repdat attribute) COUPLE (pygromos.files.blocks.imd_blocks.PRESSURESCALE attribute) COVALENTFORM (class in pygromos.files.blocks.imd_blocks) CPOR (pygromos.files.blocks.imd_blocks.POSITIONRES attribute) create_cnf() (pygromos.files.forcefield.amber.amberff.AmberFF method) (pygromos.files.forcefield.gromos.gromosff.GromosFF method) (pygromos.files.forcefield.openff.openff.OpenFF method) create_liq() (pygromos.simulations.approaches.hvap_calculation.hvap_calculation.Hvap_calculation method) create_mol2() (pygromos.files.forcefield.amber.amberff.AmberFF method) create_serenityff_nonBonded() (pygromos.files.forcefield.serenityff.serenityff.SerenityFF method) create_top() (pygromos.files.forcefield.amber.amberff.AmberFF method) (pygromos.files.forcefield.gromos.gromosff.GromosFF method) (pygromos.files.forcefield.openff.openff.OpenFF method) (pygromos.files.forcefield.serenityff.serenityff.SerenityFF method) createRDKITconf() (pygromos.files.coord.cnf.Cnf method) createVdWexclusionList() (pygromos.files.forcefield.openff.openff.OpenFF method) creteTopoFromSmiles() (pygromos.files.forcefield.gromos.gromosff.GromosFF method) CROSSDIHEDRAL (class in pygromos.files.blocks.topology_blocks) CROSSDIHEDRALH (class in pygromos.files.blocks.topology_blocks) crossgihedral_type (class in pygromos.files.blocks.topology_blocks) crossgihedralh_type (class in pygromos.files.blocks.topology_blocks)

D

DATA (pygromos.files.otherfiles.new_repdat.Repdat attribute) (pygromos.files.otherfiles.repdat.Repdat attribute) default_install() (in module pygromos.gromos.compile_gromos) DELE (pygromos.files.blocks.imd_blocks.ENERGYMIN attribute) delete_atom() (pygromos.files.blocks.pertubation_blocks.MPERTATOM method) (pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM method) (pygromos.files.blocks.topology_blocks.PERTATOMPARAM method) (pygromos.files.coord.cnf.Cnf method) delete_residue() (pygromos.files.coord.cnf.Cnf method) delete_state() (pygromos.files.blocks.pertubation_blocks.MPERTATOM method) (pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM method) (pygromos.files.blocks.topology_blocks.PERTATOMPARAM method) dens_modifier (pygromos.simulations.approaches.hvap_calculation.hvap_calculation.Hvap_calculation attribute) dfEDS (class in pygromos.analysis.free_energy_calculation) dfmult() (pygromos.gromos.gromosPP._gromosPPbase method) DFTBELEMENTS (class in pygromos.files.blocks.qmmm_blocks) (pygromos.files.qmmm.qmmm.QMMM attribute) dict_to_nice_string() (in module pygromos.utils.utils) DIHEDRAL (class in pygromos.files.blocks.topology_blocks) (pygromos.files.blocks.imd_blocks.FORCE attribute) dihedral_type (class in pygromos.files.blocks.topology_blocks) DIHEDRALH (class in pygromos.files.blocks.topology_blocks) dihedralh_type (class in pygromos.files.blocks.topology_blocks)

dihedrals (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE attribute) DIR0 (pygromos.files.blocks.imd_blocks.DISTANCERES attribute) directory_exists() (in module pygromos.utils.bash) Disres (class in pygromos.files.topology.disres) disres (pygromos.files.gromos_system.gromos_system.Gromos_System property) Distance_restraints (class in pygromos.files.topology.disres) DISTANCERES (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) DISTANCERESSPEC (class in pygromos.files.blocks.topology_blocks) distances() (pygromos.files.trajectory.trc.Trc method) distant_Restraint_Type (class in pygromos.files.blocks.topology_blocks) DLAMT (pygromos.files.blocks.imd_blocks.PERTURBATION attribute) DLI (pygromos.files.blocks.imd_blocks.LAMBDA attribute) do() (in module pygromos.simulations.hpc_queuing.job_scheduling.schedulers.simulation_scheduler) (in module pygromos.simulations.hpc_queuing.job_scheduling.workers.analysis_workers.simulation_analysis) (in module pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.clean_up_simulation_files) do_skip_job() (in module pygromos.simulations.hpc_queuing.job_scheduling.schedulers.scheduler_functions) DOFSET (pygromos.files.blocks.imd_blocks.MULTIBATH attribute) DT (pygromos.files.blocks.imd_blocks.STEP attribute) DUMMY (class in pygromos.simulations.hpc_queuing.submission_systems.dummy) DX0 (pygromos.files.blocks.imd_blocks.ENERGYMIN attribute) DXM (pygromos.files.blocks.imd_blocks.ENERGYMIN attribute) dynamic_parser() (in module pygromos.utils.utils)

E

edit_EDS() (pygromos.files.simulation_parameters.imd.Imd method) edit_REEDS() (pygromos.files.simulation_parameters.imd.Imd method) EDS (class in pygromos.files.blocks.imd_blocks) eds (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) EDS (pygromos.files.simulation_parameters.imd.Imd attribute) EDS_STAT_OUT (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) (pygromos.files.blocks.imd_blocks.REPLICA_EDS attribute) eds_subblock_names (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2015_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2020_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2021_tre_block_names_table attribute) eds_subblock_names_singleState (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2015_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2020_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2021_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_tre_block_names_table attribute) EIR (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) (pygromos.files.blocks.imd_blocks.REPLICA_EDS attribute) ELECTROSTATIC (pygromos.files.blocks.imd_blocks.FORCE attribute) ELI (pygromos.files.blocks.imd_blocks.LAMBDA attribute) emin() (in module pygromos.simulations.modules.preset_simulation_modules) end_job (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property)

ene_ana() (pygromos.gromos.gromosPP._gromosPPbase method) ENERGY03 (class in pygromos.files.trajectory.blocks.trajectory_blocks) ENERGYMIN (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) Epoti (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) Epotj (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) EPSLS (pygromos.files.blocks.imd_blocks.NONBONDED attribute) EPSRF (pygromos.files.blocks.imd_blocks.NONBONDED attribute) equation (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) (pygromos.analysis.free_energy_calculation.threeStateZwanzig attribute) (pygromos.analysis.free_energy_calculation.zwanzigEquation attribute) errLog (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property) error_estimate_class (pygromos.tests.test_analysis.test_error_estimate.test_ee attribute) error_estimator (class in pygromos.analysis.error_estimate) euler (pygromos.files.blocks.coord_blocks.GENBOX property) execute() (in module pygromos.utils.bash) execute_old() (in module pygromos.utils.bash) execute_os() (in module pygromos.utils.bash) execute_subprocess() (in module pygromos.utils.bash) extract_tar() (in module pygromos.utils.bash)

F

FACCUR (pygromos.files.blocks.imd_blocks.NONBONDED attribute) feCalculation (pygromos.tests.test_analysis.test_freeEnergy.test_BAR attribute) (pygromos.tests.test_analysis.test_freeEnergy.test_threeStateZwanzigReweighting attribute) (pygromos.tests.test_analysis.test_freeEnergy.test_ZwanzigEquation attribute) ff (pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_2016H66 attribute) (pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_54A7 attribute) (pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_forcefields attribute) field_continue_next_line (pygromos.files.blocks.mtb_blocks.mtb_fields attribute) field_seperator (pygromos.files.blocks.pertubation_blocks.TITLE attribute) fields (pygromos.files.blocks.miscBlocks.ATOMNAMELIB attribute) (pygromos.files.blocks.miscBlocks.RESIDUENAMELIB attribute) fieldseperator (pygromos.files.blocks.mtb_blocks.mtb_fields attribute) file_class (pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_forcefields attribute) (pygromos.tests.test_submission.test_hpc_queuing_submission_job.test_queuing_system attribute) (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_DUMMY attribute) (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_LOCAL attribute) (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_LSF attribute) (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_queuing_system attribute) file_exists() (in module pygromos.utils.bash) filter() (pygromos.gromos.gromosPP._gromosPPbase method) filter_atoms_from_residue() (in module pygromos.utils.pdb) find_and_unarchive_tar_files() (in module pygromos.simulations.hpc_queuing.job_scheduling.file_management) find_header() (in module pygromos.simulations.hpc_queuing.job_scheduling.file_management)

find_LJparameterNumber() (pygromos.files.topology.top.Top method) FLIM (pygromos.files.blocks.imd_blocks.ENERGYMIN attribute) FORCE (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) FORCEFIELD (class in pygromos.files.blocks.topology_blocks) (pygromos.files.blocks.mtb_blocks.LINKEXCLUSIONS attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLVENT attribute) (pygromos.files.blocks.qmmm_blocks.DFTBELEMENTS attribute) (pygromos.files.blocks.qmmm_blocks.MNDOELEMENTS attribute) (pygromos.files.blocks.qmmm_blocks.MOPACELEMENTS attribute) (pygromos.files.blocks.qmmm_blocks.ORCAELEMENTS attribute) (pygromos.files.blocks.qmmm_blocks.TURBOMOLEELEMENTS attribute) (pygromos.files.blocks.qmmm_blocks.XTBELEMENTS attribute) (pygromos.files.blocks.topology_blocks.ATOMTYPENAME attribute) (pygromos.files.blocks.topology_blocks.PHYSICALCONSTANTS attribute) (pygromos.files.blocks.topology_blocks.RESNAME attribute) (pygromos.files.blocks.topology_blocks.TOPVERSION attribute) FORCESCALE (pygromos.files.blocks.imd_blocks.DISTANCERES attribute) form_columns() (in module pygromos.utils.pdb) frameout() (pygromos.gromos.gromosPP._gromosPPbase method) FREEENERDERIVS03 (class in pygromos.files.trajectory.blocks.trajectory_blocks) full_harmonic_distance_restraint (pygromos.files.blocks.topology_blocks.distant_Restraint_Type attribute)

G

gather_simulation_file_paths() (in module pygromos.simulations.hpc_queuing.job_scheduling.file_management) gather_simulation_replica_file_paths() (in module pygromos.simulations.hpc_queuing.job_scheduling.file_management) gather_simulation_step_file_paths() (in module pygromos.simulations.hpc_queuing.job_scheduling.workers.analysis_workers.simulation_analysis) gch() (pygromos.gromos.gromosPP._gromosPPbase method) gen_possrespec() (pygromos.files.coord.cnf.Cnf method) gen_refpos() (pygromos.files.coord.cnf.Cnf method) GENBOX (class in pygromos.files.blocks.coord_blocks) (class in pygromos.files.trajectory.blocks.trajectory_blocks) (pygromos.files.coord.cnf.Cnf attribute) (pygromos.files.coord.refpos.Reference_Position attribute) general_file_tests (class in pygromos.tests.test_files.general_file_functions) generate_entry_for_frame() (pygromos.files.trajectory.trc.Trc method) generate_position_restraints() (pygromos.files.coord.cnf.Cnf method) generate_posres() (pygromos.files.gromos_system.gromos_system.Gromos_System method) generate_TITLE_entry() (pygromos.files.trajectory.trc.Trc method) geometric_code (class in pygromos.files.blocks.topology_blocks) get_all_blocks() (pygromos.files.blocks.all_blocks_class method) get_atom_coordinates() (pygromos.files.coord.cnf.Cnf method) get_atomP() (pygromos.files.coord.cnf.Cnf method) get_atoms_distance() (pygromos.files.coord.cnf.Cnf method) get_baths() (pygromos.files.trajectory.tre.Tre method) get_bondedContributions() (pygromos.files.trajectory.tre.Tre method) get_density() (in module pygromos.analysis.energy_analysis) (pygromos.files.coord.cnf.Cnf method) (pygromos.files.trajectory.tre.Tre method) get_diff_to_top() (pygromos.files.topology.top.Top method) get_dummy_cnf() (pygromos.files.trajectory.trc.Trc method) get_eds() (pygromos.files.trajectory.tre.Tre method) get_file_paths() (pygromos.files.gromos_system.gromos_system.Gromos_System method) get_gromos_coordinate_file() (pygromos.files.forcefield.amber.amberff.amber2gromos method) get_gromos_topology() (pygromos.files.forcefield.amber.amberff.amber2gromos method) get_Hvap() (in module pygromos.analysis.energy_analysis) (pygromos.files.trajectory.tre.Tre method) get_jobs_from_queue() (pygromos.simulations.hpc_queuing.submission_systems.dummy.DUMMY method) get_lambdas() (pygromos.files.trajectory.trg.Trg method) get_last_atomID() (pygromos.files.coord.cnf.Cnf method) get_LJ_parameters() (pygromos.files.forcefield.serenityff.serenityff.SerenityFF method) get_LJparameter_from_IAC() (pygromos.files.topology.top.Top method) get_mass() (pygromos.files.coord.cnf.Cnf method) (pygromos.files.topology.top.Top method) (pygromos.files.trajectory.tre.Tre method) get_mdtraj() (pygromos.files.coord.cnf.Cnf method) get_nonbondedContributions() (pygromos.files.trajectory.tre.Tre method) get_num_atomtypes() (pygromos.files.topology.top.Top method) get_pdb() (pygromos.files.coord.cnf.Cnf method) get_precalclam() (pygromos.files.trajectory.tre.Tre method) (pygromos.files.trajectory.trg.Trg method)

get_qm_engines() (pygromos.files.qmmm.qmmm.QMMM method) get_queued_jobs() (pygromos.simulations.hpc_queuing.submission_systems.lsf.LSF method) get_replica_roundtrips() (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.repdat.Repdat method) get_replica_traces() (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.repdat.Repdat method) get_replicaPosition_dependend_nup_ndown() (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.repdat.Repdat method) get_replicaPosition_dependend_nup_ndown_for_each_state() (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.repdat.Repdat method) get_residues() (pygromos.files.coord.cnf.Cnf method) get_script_generation_command() (pygromos.files.gromos_system.gromos_system.Gromos_System method) get_specialContributions() (pygromos.files.trajectory.tre.Tre method) get_submission_system() (in module pygromos.simulations.hpc_queuing.submission_systems) get_system_information() (pygromos.files.coord.cnf.Cnf method) get_temperature() (pygromos.files.trajectory.tre.Tre method) get_temperature_Info() (pygromos.files.trajectory.tre.Tre method) get_totals() (pygromos.files.trajectory.tre.Tre method) (pygromos.files.trajectory.trg.Trg method) get_totangle() (pygromos.files.trajectory.tre.Tre method) get_totbonded() (pygromos.files.trajectory.tre.Tre method) get_totcov() (pygromos.files.trajectory.tre.Tre method) get_totcrf() (pygromos.files.trajectory.tre.Tre method) get_totdihedral() (pygromos.files.trajectory.tre.Tre method) get_totene() (pygromos.files.trajectory.tre.Tre method) get_totkin() (pygromos.files.trajectory.tre.Tre method) get_totlj() (pygromos.files.trajectory.tre.Tre method) get_totnonbonded() (pygromos.files.trajectory.tre.Tre method) get_totpot() (pygromos.files.trajectory.tre.Tre method) get_volume() (pygromos.files.coord.cnf.Cnf method) get_xyz() (pygromos.files.coord.cnf.Cnf method) getAtomType() (in module pygromos.data.ff.addAtomType) getBlock() (in module pygromos.data.ff.addAtomType) gromos_2015_tre_block_names_table (class in pygromos.files.trajectory.tre_field_libs.ene_fields) gromos_2020_tre_block_names_table (class in pygromos.files.trajectory.tre_field_libs.ene_fields) gromos_2020_trg_block_names_table (class in pygromos.files.trajectory.trg) gromos_2021_tre_block_names_table (class in pygromos.files.trajectory.tre_field_libs.ene_fields) Gromos_System (class in pygromos.files.gromos_system.gromos_system) gromos_tre_block_names_table (class in pygromos.files.trajectory.tre_field_libs.ene_fields) gromosBashSyntaxParser (class in pygromos.gromos.gromosBashSyntaxParser) GromosFF (class in pygromos.files.forcefield.gromos.gromosff) GromosPP (class in pygromos.gromos.gromosPP) gromosPP (pygromos.files.gromos_system.gromos_system.Gromos_System property) gromosPP_bin_dir (pygromos.files.gromos_system.gromos_system.Gromos_System property) GromosXX (class in pygromos.gromos.gromosXX) gromosXX (pygromos.files.gromos_system.gromos_system.Gromos_System property) gromosXX_bin_dir (pygromos.files.gromos_system.gromos_system.Gromos_System property)

H

half_harmonic_attractive (pygromos.files.blocks.topology_blocks.distant_Restraint_Type attribute) half_harmonic_repulsive (pygromos.files.blocks.topology_blocks.distant_Restraint_Type attribute)

harmonic2quarticAngleConversion() (pygromos.files.topology.top.Top method) help_class (pygromos.tests.test_files.test_trajectory.test_trc attribute) Hvap_calculation (class in pygromos.simulations.approaches.hvap_calculation.hvap_calculation)

I

ID (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) Ifp (class in pygromos.files.topology.ifp) IG (pygromos.files.blocks.imd_blocks.INITIALISE attribute) Imd (class in pygromos.files.simulation_parameters.imd) imd (pygromos.files.gromos_system.gromos_system.Gromos_System property) IMPDIHEDRAL (class in pygromos.files.blocks.topology_blocks) impdihedral_type (class in pygromos.files.blocks.topology_blocks) IMPDIHEDRALH (class in pygromos.files.blocks.topology_blocks) impdihedralh_type (class in pygromos.files.blocks.topology_blocks) IMPDIHEDRALTYPE (class in pygromos.files.blocks.topology_blocks) impdihedraltype_type (class in pygromos.files.blocks.topology_blocks) IMPDIHEDRALTYPECODE (class in pygromos.files.blocks.topology_blocks) IMPROPER (pygromos.files.blocks.imd_blocks.FORCE attribute) improper_dihedral_type (class in pygromos.files.blocks.topology_blocks) improper_dihedrals (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE attribute) in_file2_path (pygromos.tests.test_files.test_trajectory.test_tre attribute) in_file_eds_path (pygromos.tests.test_files.test_trajectory.test_tre attribute) in_file_h5_path (pygromos.tests.test_files.test_trajectory.test_tre attribute) (pygromos.tests.test_files.test_trajectory.test_trg attribute) (pygromos.tests.test_files.test_trajectory.traj_standard_tests attribute) in_file_lam_path (pygromos.tests.test_files.test_trajectory.test_tre attribute) in_file_path (pygromos.tests.test_files.test_cnf_funcs.test_cnf attribute) (pygromos.tests.test_files.test_disres.test_disres attribute) (pygromos.tests.test_files.test_disres_file.test_disres attribute) (pygromos.tests.test_files.test_imd.test_imd attribute) (pygromos.tests.test_files.test_mtb.test_mtb attribute) (pygromos.tests.test_files.test_mtb.test_mtb_g54a7 attribute) (pygromos.tests.test_files.test_mtb.test_mtb_orga attribute) (pygromos.tests.test_files.test_ptp.test_ptp attribute) (pygromos.tests.test_files.test_qmmm.test_qmmm attribute) (pygromos.tests.test_files.test_qmmm.test_qmmm_imd attribute) (pygromos.tests.test_files.test_repdat.test_repdat attribute) (pygromos.tests.test_files.test_resnlib.test_resnlib attribute) (pygromos.tests.test_files.test_top.test_top attribute) (pygromos.tests.test_files.test_top.test_top_simple attribute) (pygromos.tests.test_files.test_trajectory.test_trc attribute) (pygromos.tests.test_files.test_trajectory.test_tre attribute) (pygromos.tests.test_files.test_trajectory.test_trg attribute) (pygromos.tests.test_files.test_trajectory.traj_standard_tests attribute)

in_file_path_h5 (pygromos.tests.test_files.test_trajectory.test_trc attribute) in_file_w_genbox_cnf_path (pygromos.tests.test_files.test_trajectory.test_trc attribute) in_file_w_genbox_path (pygromos.tests.test_files.test_trajectory.test_trc attribute) INITIALISE (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) INNERLOOP (class in pygromos.files.blocks.imd_blocks) input_cnf_path (pygromos.tests.test_files.test_gromosSystem.test_gromos_system attribute) (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks attribute) input_top_path (pygromos.tests.test_files.test_gromosSystem.test_gromos_system attribute) (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks attribute) install_gromos() (in module pygromos.gromos.compile_gromos) ion() (pygromos.gromos.gromosPP._gromosPPbase method) IRBATH (pygromos.files.blocks.imd_blocks.MULTIBATH attribute) is_directory() (in module pygromos.utils.bash) is_file() (in module pygromos.utils.bash)

J

job_queue_list (pygromos.simulations.hpc_queuing.submission_systems.dummy.DUMMY attribute) (pygromos.simulations.hpc_queuing.submission_systems.local.LOCAL attribute) jobGroup (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property) jobID (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property)

jobLim (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property) jobName (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property) JVAL (class in pygromos.files.otherfiles.noe_output) jval() (pygromos.gromos.gromosPP._gromosPPbase method)

K

k (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) (pygromos.analysis.free_energy_calculation.threeStateZwanzig attribute) (pygromos.analysis.free_energy_calculation.zwanzigEquation attribute)

KCUT (pygromos.files.blocks.imd_blocks.NONBONDED attribute) kill_jobs() (pygromos.simulations.hpc_queuing.submission_systems.lsf.LSF method)

L

lam (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) (pygromos.files.blocks.coord_blocks.PERTDATA property) lam_subblock_names (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2015_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2020_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2021_tre_block_names_table attribute) lam_subblock_names_singleLam (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2015_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2020_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2021_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_tre_block_names_table attribute) LAMBDA (class in pygromos.files.blocks.imd_blocks) LAST (pygromos.files.blocks.imd_blocks.MULTIBATH attribute) lattice_shift (class in pygromos.files.blocks.coord_blocks) LATTICESHIFTS (class in pygromos.files.blocks.coord_blocks) (pygromos.files.coord.cnf.Cnf attribute) (pygromos.files.coord.posres.Position_Restraints attribute) (pygromos.files.coord.refpos.Reference_Position attribute) length (pygromos.files.blocks.coord_blocks.GENBOX property)

li (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) line_seperator (pygromos.files.blocks.pertubation_blocks.TITLE attribute) lineseperator (pygromos.files.blocks.mtb_blocks.mtb_fields attribute) link_folder() (in module pygromos.utils.bash) LINKEXCLUSIONS (class in pygromos.files.blocks.mtb_blocks) lj (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) lj_exceptions (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE attribute) ljexception_type (class in pygromos.files.blocks.topology_blocks) LJEXCEPTIONS (class in pygromos.files.blocks.topology_blocks) LJPARAMETERS (class in pygromos.files.blocks.topology_blocks) ljparameters_type (class in pygromos.files.blocks.topology_blocks) load() (pygromos.files.gromos_system.gromos_system.Gromos_System class method) (pygromos.files.trajectory.trc.Trc class method) LOCAL (class in pygromos.simulations.hpc_queuing.submission_systems.local) LRESCALE (pygromos.files.blocks.imd_blocks.REPLICA attribute) LSF (class in pygromos.simulations.hpc_queuing.submission_systems.lsf)

M

main() (in module pygromos.data.ff.addAtomType) make_folder() (in module pygromos.utils.bash) make_ordered() (pygromos.files.topology.top.Top method) make_top() (pygromos.gromos.gromosPP._gromosPPbase method) make_topolog() (in module pygromos.files.topology.top) MAKETOPVERSION (class in pygromos.files.blocks.topology_blocks) (pygromos.files.blocks.mtb_blocks.LINKEXCLUSIONS attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLVENT attribute) (pygromos.files.blocks.qmmm_blocks.DFTBELEMENTS attribute) (pygromos.files.blocks.qmmm_blocks.MNDOELEMENTS attribute) (pygromos.files.blocks.qmmm_blocks.MOPACELEMENTS attribute) (pygromos.files.blocks.qmmm_blocks.ORCAELEMENTS attribute) (pygromos.files.blocks.qmmm_blocks.TURBOMOLEELEMENTS attribute) (pygromos.files.blocks.qmmm_blocks.XTBELEMENTS attribute) (pygromos.files.blocks.topology_blocks.ATOMTYPENAME attribute) (pygromos.files.blocks.topology_blocks.PHYSICALCONSTANTS attribute) (pygromos.files.blocks.topology_blocks.RESNAME attribute) (pygromos.files.blocks.topology_blocks.TOPVERSION attribute) mass (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) MASSATOMTYPECODE (class in pygromos.files.blocks.topology_blocks) max_iterations (pygromos.analysis.free_energy_calculation.bar attribute) (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) MAXLAM (pygromos.files.blocks.imd_blocks.PRECALCLAM attribute) md() (in module pygromos.simulations.modules.preset_simulation_modules) md_run() (pygromos.gromos.gromosXX._GromosXX method) min_iterations (pygromos.analysis.free_energy_calculation.bar attribute) (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) MINLAM (pygromos.files.blocks.imd_blocks.PRECALCLAM attribute) mixed_atom_lj_pair_type (class in pygromos.files.blocks.topology_blocks) MIXEDATOMLJPAIR (class in pygromos.files.blocks.topology_blocks) MMSCAL (pygromos.files.blocks.imd_blocks.QMMM attribute) MNDOELEMENTS (class in pygromos.files.blocks.qmmm_blocks) (pygromos.files.qmmm.qmmm.QMMM attribute) module pygromos pygromos.analysis pygromos.analysis.coordinate_analysis pygromos.analysis.energy_analysis pygromos.analysis.error_estimate pygromos.analysis.free_energy_calculation pygromos.data pygromos.data.ene_ana_libs pygromos.data.ff pygromos.data.ff.addAtomType pygromos.data.ff.atomType pygromos.data.ff.Gromos2016H66 pygromos.data.ff.Gromos54A7 pygromos.data.ff.MixHexGromos54A7 pygromos.data.simulation_parameters_templates pygromos.data.solvent_coordinates pygromos.data.topology_templates pygromos.files pygromos.files.blocks pygromos.files.blocks.coord_blocks pygromos.files.blocks.imd_blocks pygromos.files.blocks.miscBlocks pygromos.files.blocks.mtb_blocks pygromos.files.blocks.pertubation_blocks pygromos.files.blocks.qmmm_blocks pygromos.files.blocks.replica_exchange_blocks pygromos.files.blocks.topology_blocks pygromos.files.coord pygromos.files.coord.cnf pygromos.files.coord.posres pygromos.files.coord.refpos pygromos.files.forcefield pygromos.files.forcefield.amber pygromos.files.forcefield.amber.amberff pygromos.files.forcefield.gromos pygromos.files.forcefield.gromos.gromosff pygromos.files.forcefield.openff pygromos.files.forcefield.openff.openff pygromos.files.forcefield.serenityff pygromos.files.forcefield.serenityff.serenityff pygromos.files.forcefield.serenityff.serenityff_data pygromos.files.gromos_system pygromos.files.gromos_system.gromos_system pygromos.files.otherfiles pygromos.files.otherfiles.new_repdat pygromos.files.otherfiles.noe_output pygromos.files.otherfiles.repdat pygromos.files.otherfiles.residue_library pygromos.files.qmmm pygromos.files.qmmm.qmmm pygromos.files.simulation_parameters pygromos.files.simulation_parameters.imd pygromos.files.topology pygromos.files.topology.disres pygromos.files.topology.ifp pygromos.files.topology.mtb pygromos.files.topology.ptp pygromos.files.topology.top pygromos.files.trajectory pygromos.files.trajectory.blocks pygromos.files.trajectory.blocks.energy_trajectory_subblock pygromos.files.trajectory.blocks.trajectory_blocks pygromos.files.trajectory.trc pygromos.files.trajectory.tre pygromos.files.trajectory.tre_field_libs pygromos.files.trajectory.tre_field_libs.ene_fields pygromos.files.trajectory.trg pygromos.gromos pygromos.gromos.compile_gromos pygromos.gromos.gromosBashSyntaxParser pygromos.gromos.gromosPP pygromos.gromos.gromosXX pygromos.gromos.pyGromosPP pygromos.gromos.pyGromosPP.com_top pygromos.gromos.pyGromosPP.ran_box pygromos.pygromos pygromos.simulations pygromos.simulations.approaches pygromos.simulations.approaches.hvap_calculation pygromos.simulations.approaches.hvap_calculation.hvap_calculation pygromos.simulations.approaches.hvap_calculation.hvap_input_files pygromos.simulations.hpc_queuing pygromos.simulations.hpc_queuing.job_scheduling pygromos.simulations.hpc_queuing.job_scheduling.file_management pygromos.simulations.hpc_queuing.job_scheduling.module_functions pygromos.simulations.hpc_queuing.job_scheduling.schedulers pygromos.simulations.hpc_queuing.job_scheduling.schedulers.scheduler_functions pygromos.simulations.hpc_queuing.job_scheduling.schedulers.simulation_scheduler pygromos.simulations.hpc_queuing.job_scheduling.workers pygromos.simulations.hpc_queuing.job_scheduling.workers.analysis_workers pygromos.simulations.hpc_queuing.job_scheduling.workers.analysis_workers.simulation_analysis pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.clean_up_simulation_files pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.simulation_run_worker pygromos.simulations.hpc_queuing.submission_systems pygromos.simulations.hpc_queuing.submission_systems.dummy pygromos.simulations.hpc_queuing.submission_systems.local pygromos.simulations.hpc_queuing.submission_systems.lsf pygromos.simulations.hpc_queuing.submission_systems.submission_job pygromos.simulations.modules pygromos.simulations.modules.general_analysis_modules pygromos.simulations.modules.general_simulation_modules pygromos.simulations.modules.preset_simulation_modules pygromos.simulations.modules.ti_modules pygromos.tests pygromos.tests.in_testfiles pygromos.tests.out_testresults pygromos.tests.test_analysis pygromos.tests.test_analysis.test_error_estimate pygromos.tests.test_analysis.test_freeEnergy pygromos.tests.test_approaches pygromos.tests.test_approaches.test_solvation_free_ernergy pygromos.tests.test_files pygromos.tests.test_files.general_file_functions pygromos.tests.test_files.test_cnf_funcs pygromos.tests.test_files.test_disres pygromos.tests.test_files.test_disres_file pygromos.tests.test_files.test_gromosSystem pygromos.tests.test_files.test_gromosSystem_forcefields pygromos.tests.test_files.test_imd pygromos.tests.test_files.test_imd_block pygromos.tests.test_files.test_mtb pygromos.tests.test_files.test_ptp pygromos.tests.test_files.test_qmmm pygromos.tests.test_files.test_repdat pygromos.tests.test_files.test_resnlib pygromos.tests.test_files.test_top pygromos.tests.test_files.test_trajectory pygromos.tests.test_pygromos pygromos.tests.test_simulation_blocks pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks pygromos.tests.test_submission pygromos.tests.test_submission.test_hpc_queuing_submission_job pygromos.tests.test_submission.test_hpc_queuing_submission_scheduling pygromos.tests.test_submission.test_hpc_queuing_submission_systems pygromos.utils pygromos.utils.amino_acids pygromos.utils.bash pygromos.utils.compiledProgram pygromos.utils.pdb pygromos.utils.typing pygromos.utils.utils pygromos.visualization pygromos.visualization.coordinates_visualization

moleculeSliceParser() (pygromos.gromos.gromosBashSyntaxParser.gromosBashSyntaxParser static method) MOPACELEMENTS (class in pygromos.files.blocks.qmmm_blocks) (pygromos.files.qmmm.qmmm.QMMM attribute) move_file() (in module pygromos.utils.bash) MPERATOM (pygromos.files.topology.ptp.Pertubation_topology attribute) (pygromos.files.topology.ptp.Ptp attribute) MPERTATOM (class in pygromos.files.blocks.pertubation_blocks) Mtb (class in pygromos.files.topology.mtb) mtb_angles_field (class in pygromos.files.blocks.mtb_blocks) mtb_atoms_field (class in pygromos.files.blocks.mtb_blocks) mtb_atoms_solvent_field (class in pygromos.files.blocks.mtb_blocks) mtb_blocks (class in pygromos.files.blocks.mtb_blocks) mtb_bonds_field (class in pygromos.files.blocks.mtb_blocks) mtb_constraints_field (class in pygromos.files.blocks.mtb_blocks) mtb_dihedral_field (class in pygromos.files.blocks.mtb_blocks) mtb_ends (pygromos.files.topology.mtb.Mtb attribute) mtb_fields (class in pygromos.files.blocks.mtb_blocks) mtb_lj_exceptions_field (class in pygromos.files.blocks.mtb_blocks) mtb_preceding_exclusions_field (class in pygromos.files.blocks.mtb_blocks) mtb_solutes (pygromos.files.topology.mtb.Mtb attribute) mtb_solvents (pygromos.files.topology.mtb.Mtb attribute) mtb_trailing_atoms_field (class in pygromos.files.blocks.mtb_blocks) MTBUILDBLEND (class in pygromos.files.blocks.mtb_blocks) MTBUILDBLSOLUTE (class in pygromos.files.blocks.mtb_blocks) MTBUILDBLSOLVENT (class in pygromos.files.blocks.mtb_blocks) MULTIBATH (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) multiply_top() (pygromos.files.topology.top.Top method) multiplyArgumentParser() (pygromos.gromos.gromosBashSyntaxParser.gromosBashSyntaxParser static method)

N

NA2CLC (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NALIAS (pygromos.files.blocks.imd_blocks.NONBONDED attribute) name (pygromos.files.blocks.imd_blocks.AMBER attribute) (pygromos.files.blocks.imd_blocks.BOUNDCOND attribute) (pygromos.files.blocks.imd_blocks.COMTRANSROT attribute) (pygromos.files.blocks.imd_blocks.CONSTRAINT attribute) (pygromos.files.blocks.imd_blocks.COVALENTFORM attribute) (pygromos.files.blocks.imd_blocks.DISTANCERES attribute) (pygromos.files.blocks.imd_blocks.ENERGYMIN attribute) (pygromos.files.blocks.imd_blocks.FORCE attribute) (pygromos.files.blocks.imd_blocks.INITIALISE attribute) (pygromos.files.blocks.imd_blocks.INNERLOOP attribute) (pygromos.files.blocks.imd_blocks.LAMBDA attribute) (pygromos.files.blocks.imd_blocks.MULTIBATH attribute) (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) (pygromos.files.blocks.imd_blocks.NONBONDED attribute) (pygromos.files.blocks.imd_blocks.PAIRLIST attribute) (pygromos.files.blocks.imd_blocks.PERTURBATION attribute) (pygromos.files.blocks.imd_blocks.POSITIONRES attribute) (pygromos.files.blocks.imd_blocks.PRECALCLAM attribute) (pygromos.files.blocks.imd_blocks.PRESSURESCALE attribute) (pygromos.files.blocks.imd_blocks.PRINTOUT attribute) (pygromos.files.blocks.imd_blocks.QMMM attribute) (pygromos.files.blocks.imd_blocks.RANDOMNUMBERS attribute) (pygromos.files.blocks.imd_blocks.REPLICA attribute) (pygromos.files.blocks.imd_blocks.REPLICA_EDS attribute) (pygromos.files.blocks.imd_blocks.ROTTRANS attribute) (pygromos.files.blocks.imd_blocks.STEP attribute) (pygromos.files.blocks.imd_blocks.STOCHDYN attribute) (pygromos.files.blocks.imd_blocks.SYSTEM attribute) (pygromos.files.blocks.imd_blocks.WRITETRAJ attribute) NAME (pygromos.files.blocks.topology_blocks.FORCEFIELD attribute) name (pygromos.files.gromos_system.gromos_system.Gromos_System property) (pygromos.utils.amino_acids.amino_acid attribute) NASORD (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NBATHS (pygromos.files.blocks.imd_blocks.MULTIBATH attribute) NBON (pygromos.files.blocks.qmmm_blocks.QMZONE attribute) (pygromos.files.blocks.topology_blocks.BOND attribute) NBONH (pygromos.files.blocks.topology_blocks.BONDH attribute) NBREF (pygromos.files.blocks.imd_blocks.STOCHDYN attribute) NBTY (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPE attribute) (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPE attribute) (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPECODE attribute) NCON (pygromos.files.blocks.topology_blocks.CONSTRAINT attribute) NCONS (pygromos.files.blocks.topology_blocks.SOLVENTCONSTR attribute) NCYC (pygromos.files.blocks.imd_blocks.ENERGYMIN attribute) NDFMIN (pygromos.files.blocks.imd_blocks.BOUNDCOND attribute) NEGR (pygromos.files.blocks.imd_blocks.FORCE attribute) NEOFF (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) NEW_REPLICA_EDS (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) NEX (pygromos.files.blocks.topology_blocks.LJEXCEPTIONS attribute) NFDORD (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NGPUS (pygromos.files.blocks.imd_blocks.INNERLOOP attribute) NGX (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NGY (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NGZ (pygromos.files.blocks.imd_blocks.NONBONDED attribute) nice_s_vals() (in module pygromos.utils.utils) NILG1 (pygromos.files.blocks.imd_blocks.LAMBDA attribute) NILG2 (pygromos.files.blocks.imd_blocks.LAMBDA attribute) NKX (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NKY (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NKZ (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NLAM (pygromos.files.blocks.imd_blocks.PERTURBATION attribute) NLRELE (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NLRLJ (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NMATY (pygromos.files.blocks.topology_blocks.MASSATOMTYPECODE attribute) NMIN (pygromos.files.blocks.imd_blocks.ENERGYMIN attribute) NOE (class in pygromos.files.otherfiles.noe_output) noe() (pygromos.gromos.gromosPP._gromosPPbase method) NOE_VIOLATIONS (pygromos.files.otherfiles.noe_output.NOE attribute) non_ligand_info (pygromos.files.gromos_system.gromos_system.Gromos_System attribute) non_ligand_infos (in module pygromos.files.coord.cnf) NONBONDED (class in pygromos.files.blocks.imd_blocks) nonbonded (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) NONBONDED (pygromos.files.simulation_parameters.imd.Imd attribute) NPHI (pygromos.files.blocks.topology_blocks.CROSSDIHEDRAL attribute) (pygromos.files.blocks.topology_blocks.DIHEDRAL attribute) NPHIH (pygromos.files.blocks.topology_blocks.CROSSDIHEDRALH attribute) (pygromos.files.blocks.topology_blocks.DIHEDRALH attribute) NPM (pygromos.files.blocks.imd_blocks.SYSTEM attribute) NPTY (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPE attribute) (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPECODE attribute) NQEVAL (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NQHI (pygromos.files.blocks.topology_blocks.IMPDIHEDRAL attribute) NQHIH (pygromos.files.blocks.topology_blocks.IMPDIHEDRALH attribute) NQTY (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPE attribute) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPECODE attribute) NRAM (pygromos.files.blocks.topology_blocks.SOLVENTATOM attribute) NRATT (pygromos.files.blocks.topology_blocks.SINGLEATOMLJPAIR attribute) NRATT2 (pygromos.files.blocks.topology_blocks.LJPARAMETERS attribute) NRBTY (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPECODE attribute) NRDGL (pygromos.files.blocks.imd_blocks.PERTURBATION attribute) NRDGRD (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NRE (pygromos.files.blocks.imd_blocks.FORCE attribute) NRELAM (pygromos.files.blocks.imd_blocks.REPLICA attribute) NREQUIL (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) (pygromos.files.blocks.imd_blocks.REPLICA attribute) (pygromos.files.blocks.imd_blocks.REPLICA_EDS attribute) NRES (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) (pygromos.files.blocks.imd_blocks.REPLICA_EDS attribute) NRET (pygromos.files.blocks.imd_blocks.REPLICA attribute) NRETRIAL (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) (pygromos.files.blocks.imd_blocks.REPLICA attribute) (pygromos.files.blocks.imd_blocks.REPLICA_EDS attribute)

NRLAM (pygromos.files.blocks.imd_blocks.PRECALCLAM attribute) NRMATY (pygromos.files.blocks.topology_blocks.MASSATOMTYPECODE attribute) NRMTT (pygromos.files.blocks.topology_blocks.MIXEDATOMLJPAIR attribute) NRNE (pygromos.files.blocks.mtb_blocks.LINKEXCLUSIONS attribute) NRP (pygromos.files.blocks.topology_blocks.SOLUTEATOM attribute) NRPTY (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPECODE attribute) NRQTY (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPECODE attribute) NRST (pygromos.files.blocks.topology_blocks.SPECATOMLJPAIR attribute) NRTTY (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPECODE attribute) NSCALE (pygromos.files.blocks.imd_blocks.PERTURBATION attribute) NSCM (pygromos.files.blocks.imd_blocks.COMTRANSROT attribute) NSFR (pygromos.files.blocks.imd_blocks.STOCHDYN attribute) NSHAPE (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NSLFEXCL (pygromos.files.blocks.imd_blocks.NONBONDED attribute) NSM (pygromos.files.blocks.imd_blocks.SYSTEM attribute) (pygromos.files.blocks.topology_blocks.PRESSUREGROUPS attribute) (pygromos.files.blocks.topology_blocks.SOLUTEMOLECULES attribute) (pygromos.files.blocks.topology_blocks.TEMPERATUREGROUPS attribute) NSNB (pygromos.files.blocks.imd_blocks.PAIRLIST attribute) NSP (pygromos.files.blocks.topology_blocks.PRESSUREGROUPS attribute) (pygromos.files.blocks.topology_blocks.SOLUTEMOLECULES attribute) (pygromos.files.blocks.topology_blocks.TEMPERATUREGROUPS attribute) NSPORD (pygromos.files.blocks.imd_blocks.NONBONDED attribute) nStates (pygromos.files.blocks.pertubation_blocks.MPERTATOM property) (pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM property) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLE property) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLEH property) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCH property) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCHH property) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIH property) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIHH property) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIH property) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH property) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH.PERTPROPERDIH property) (pygromos.files.blocks.topology_blocks.PERTATOMPARAM property) NSTLIM (pygromos.files.blocks.imd_blocks.STEP attribute) NTB (pygromos.files.blocks.imd_blocks.BOUNDCOND attribute) NTBAH (pygromos.files.blocks.imd_blocks.COVALENTFORM attribute) NTBBH (pygromos.files.blocks.imd_blocks.COVALENTFORM attribute) NTBDN (pygromos.files.blocks.imd_blocks.COVALENTFORM attribute) NTC (pygromos.files.blocks.imd_blocks.CONSTRAINT attribute) NTCP (pygromos.files.blocks.imd_blocks.CONSTRAINT attribute) NTCP0 (pygromos.files.blocks.imd_blocks.CONSTRAINT attribute) NTCS (pygromos.files.blocks.imd_blocks.CONSTRAINT attribute) NTCS0 (pygromos.files.blocks.imd_blocks.CONSTRAINT attribute) NTDIR (pygromos.files.blocks.imd_blocks.DISTANCERES attribute) NTDIRA (pygromos.files.blocks.imd_blocks.DISTANCERES attribute) NTEM (pygromos.files.blocks.imd_blocks.ENERGYMIN attribute) NTFR (pygromos.files.blocks.imd_blocks.STOCHDYN attribute) NTG (pygromos.files.blocks.imd_blocks.PERTURBATION attribute) NTGSL (pygromos.files.blocks.imd_blocks.RANDOMNUMBERS attribute) NTHE (pygromos.files.blocks.topology_blocks.BONDANGLE attribute) NTHEH (pygromos.files.blocks.topology_blocks.BONDANGLEH attribute) NTICOM (pygromos.files.blocks.imd_blocks.INITIALISE attribute) NTIL (pygromos.files.blocks.imd_blocks.LAMBDA attribute) NTILM (pygromos.files.blocks.imd_blocks.INNERLOOP attribute) NTILS (pygromos.files.blocks.imd_blocks.INNERLOOP attribute) NTINHB (pygromos.files.blocks.imd_blocks.INITIALISE attribute) NTINHT (pygromos.files.blocks.imd_blocks.INITIALISE attribute) NTIRTC (pygromos.files.blocks.imd_blocks.INITIALISE attribute) NTISHI (pygromos.files.blocks.imd_blocks.INITIALISE attribute) NTISHK (pygromos.files.blocks.imd_blocks.INITIALISE attribute) NTISTI (pygromos.files.blocks.imd_blocks.INITIALISE attribute) NTIVEL (pygromos.files.blocks.imd_blocks.INITIALISE attribute) NTLI (pygromos.files.blocks.imd_blocks.LAMBDA attribute) nTotalStateAtoms (pygromos.files.blocks.pertubation_blocks.MPERTATOM property) (pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM property) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLE property) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLEH property) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCH property) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCHH property) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIH property) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIHH property) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIH property) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH property) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH.PERTPROPERDIH property) (pygromos.files.blocks.topology_blocks.PERTATOMPARAM property) NTPOR (pygromos.files.blocks.imd_blocks.POSITIONRES attribute) NTPORB (pygromos.files.blocks.imd_blocks.POSITIONRES attribute) NTPORS (pygromos.files.blocks.imd_blocks.POSITIONRES attribute) NTPP (pygromos.files.blocks.imd_blocks.PRINTOUT attribute) NTPR (pygromos.files.blocks.imd_blocks.PRINTOUT attribute) NTQMMM (pygromos.files.blocks.imd_blocks.QMMM attribute) NTQMSW (pygromos.files.blocks.imd_blocks.QMMM attribute) NTRNG (pygromos.files.blocks.imd_blocks.RANDOMNUMBERS attribute) NTSD (pygromos.files.blocks.imd_blocks.STOCHDYN attribute) NTTY (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPECODE attribute) NTWB (pygromos.files.blocks.imd_blocks.WRITETRAJ attribute) NTWDIR (pygromos.files.blocks.imd_blocks.DISTANCERES attribute) NTWE (pygromos.files.blocks.imd_blocks.WRITETRAJ attribute) NTWF (pygromos.files.blocks.imd_blocks.WRITETRAJ attribute) NTWG (pygromos.files.blocks.imd_blocks.WRITETRAJ attribute) NTWQMMM (pygromos.files.blocks.imd_blocks.QMMM attribute) NTWSE (pygromos.files.blocks.imd_blocks.WRITETRAJ attribute) NTWV (pygromos.files.blocks.imd_blocks.WRITETRAJ attribute) NTWX (pygromos.files.blocks.imd_blocks.WRITETRAJ attribute) NUM (pygromos.files.blocks.imd_blocks.MULTIBATH attribute) number_of_atoms (pygromos.tests.test_approaches.test_solvation_free_ernergy.test_sfe attribute) numFullAtomistic (pygromos.utils.amino_acids.amino_acid attribute) NUMSTATES (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) (pygromos.files.blocks.imd_blocks.REPLICA_EDS attribute) numUnitedAtoms (pygromos.utils.amino_acids.amino_acid attribute) NWRGRD (pygromos.files.blocks.imd_blocks.NONBONDED attribute)

O

oneLetter (pygromos.utils.amino_acids.amino_acid attribute) OpenFF (class in pygromos.files.forcefield.openff.openff) optional_files (pygromos.files.gromos_system.gromos_system.Gromos_System attribute) ORCAELEMENTS (class in pygromos.files.blocks.qmmm_blocks) (pygromos.files.qmmm.qmmm.QMMM attribute) order (pygromos.files.blocks.pertubation_blocks.TITLE attribute)

origin (pygromos.files.blocks.coord_blocks.GENBOX property) outLog (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property) outpath (pygromos.tests.test_files.test_trajectory.test_trc attribute) (pygromos.tests.test_files.test_trajectory.test_tre attribute) (pygromos.tests.test_files.test_trajectory.test_trg attribute) (pygromos.tests.test_files.test_trajectory.traj_standard_tests attribute)

P

p (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) PAIRLIST (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) parmchk() (pygromos.files.forcefield.amber.amberff.amber2gromos method) parse_attribute_files() (pygromos.files.gromos_system.gromos_system.Gromos_System method) parse_csv_energy_trajectories() (in module pygromos.simulations.hpc_queuing.job_scheduling.file_management) parse_csv_energy_trajectory() (in module pygromos.simulations.hpc_queuing.job_scheduling.file_management) parse_trc_efficiently() (pygromos.files.trajectory.trc.Trc method) partner (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) path (pygromos.files.coord.posres.Position_Restraints attribute) (pygromos.files.coord.refpos.Reference_Position attribute) (pygromos.files.qmmm.qmmm.QMMM attribute) (pygromos.files.simulation_parameters.imd.Imd attribute) (pygromos.files.topology.ifp.Ifp attribute) (pygromos.files.topology.ptp.Ptp attribute) (pygromos.files.trajectory.trc.Trc attribute) path_exists() (in module pygromos.utils.bash) Pbc (class in pygromos.files.blocks.coord_blocks) pbc (pygromos.files.blocks.coord_blocks.GENBOX property) pdb2gromos() (pygromos.gromos.gromosPP._gromosPPbase method) pdb2seq() (pygromos.gromos.gromosPP._gromosPPbase method) pdb_top (pygromos.files.blocks.miscBlocks.ATOMNAMELIB attribute) (pygromos.files.blocks.miscBlocks.RESIDUENAMELIB attribute) PERIODIC (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) periodic_distance() (in module pygromos.analysis.coordinate_analysis) periodic_shift() (in module pygromos.analysis.coordinate_analysis) PERTATOMPARAM (class in pygromos.files.blocks.pertubation_blocks) (class in pygromos.files.blocks.topology_blocks) (pygromos.files.topology.ptp.Pertubation_topology attribute) (pygromos.files.topology.ptp.Ptp attribute) PERTBONDANGLE (class in pygromos.files.blocks.pertubation_blocks) (pygromos.files.topology.ptp.Pertubation_topology attribute) (pygromos.files.topology.ptp.Ptp attribute) PERTBONDANGLEH (class in pygromos.files.blocks.pertubation_blocks) (pygromos.files.topology.ptp.Pertubation_topology attribute) (pygromos.files.topology.ptp.Ptp attribute) PERTBONDSTRETCH (class in pygromos.files.blocks.pertubation_blocks) (pygromos.files.topology.ptp.Pertubation_topology attribute) (pygromos.files.topology.ptp.Ptp attribute) PERTBONDSTRETCHH (class in pygromos.files.blocks.pertubation_blocks) (pygromos.files.topology.ptp.Pertubation_topology attribute) (pygromos.files.topology.ptp.Ptp attribute) PERTDATA (class in pygromos.files.blocks.coord_blocks) (pygromos.files.coord.cnf.Cnf attribute) PERTIMROPERDIH (class in pygromos.files.blocks.pertubation_blocks) PERTIMROPERDIHH (class in pygromos.files.blocks.pertubation_blocks) PERTPROPERDIH (class in pygromos.files.blocks.pertubation_blocks) (pygromos.files.topology.ptp.Pertubation_topology attribute) (pygromos.files.topology.ptp.Ptp attribute) PERTPROPERDIHH (class in pygromos.files.blocks.pertubation_blocks) PERTPROPERDIHH.PERTPROPERDIH (class in pygromos.files.blocks.pertubation_blocks) Pertubation_topology (class in pygromos.files.topology.ptp) PERTURBATION (class in pygromos.files.blocks.imd_blocks) PHYSICALCONSTANTS (class in pygromos.files.blocks.topology_blocks) POSITION (class in pygromos.files.blocks.coord_blocks) (pygromos.files.coord.cnf.Cnf attribute) Position_Restraints (class in pygromos.files.coord.posres) POSITIONRED (class in pygromos.files.trajectory.blocks.trajectory_blocks) POSITIONRES (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) posres (pygromos.files.gromos_system.gromos_system.Gromos_System property) POSRESSPEC (class in pygromos.files.blocks.coord_blocks) (pygromos.files.coord.posres.Position_Restraints attribute) post_execution_command (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property) PRECALCLAM (class in pygromos.files.blocks.imd_blocks) precalclam (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) precalclam_subblock (pygromos.files.trajectory.trg.gromos_2020_trg_block_names_table attribute) preceding_exclusions (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE attribute) prep_eds() (pygromos.gromos.gromosPP._gromosPPbase method) prep_noe() (pygromos.gromos.gromosPP._gromosPPbase method) prepare_for_simulation() (pygromos.files.gromos_system.gromos_system.Gromos_System method) PRES0 (pygromos.files.blocks.imd_blocks.PRESSURESCALE attribute) pressure (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) PRESSUREGROUPS (class in pygromos.files.blocks.topology_blocks) PRESSURESCALE (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) PRINTOUT (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) project_concatenation() (in module pygromos.simulations.hpc_queuing.job_scheduling.file_management) (in module pygromos.simulations.hpc_queuing.job_scheduling.workers.analysis_workers.simulation_analysis) protein_info (pygromos.files.gromos_system.gromos_system.Gromos_System attribute) protein_infos (in module pygromos.files.coord.cnf) pseudo_H_atom_goc_H_atoms_CH3 (pygromos.files.blocks.topology_blocks.geometric_code attribute) pseudo_H_atoms_goc_of_three_CH3 (pygromos.files.blocks.topology_blocks.geometric_code attribute) pseudo_H_atoms_goc_of_two_CH3 (pygromos.files.blocks.topology_blocks.geometric_code attribute) Ptp (class in pygromos.files.topology.ptp) ptp (pygromos.files.gromos_system.gromos_system.Gromos_System property) pygromos module pygromos.analysis module pygromos.analysis.coordinate_analysis module pygromos.analysis.energy_analysis module pygromos.analysis.error_estimate module pygromos.analysis.free_energy_calculation module pygromos.data module pygromos.data.ene_ana_libs module pygromos.data.ff module pygromos.data.ff.addAtomType module pygromos.data.ff.atomType module pygromos.data.ff.Gromos2016H66 module pygromos.data.ff.Gromos54A7 module pygromos.data.ff.MixHexGromos54A7 module pygromos.data.simulation_parameters_templates module pygromos.data.solvent_coordinates module pygromos.data.topology_templates module pygromos.files module pygromos.files.blocks module pygromos.files.blocks.coord_blocks module pygromos.files.blocks.imd_blocks module pygromos.files.blocks.miscBlocks module pygromos.files.blocks.mtb_blocks module pygromos.files.blocks.pertubation_blocks module pygromos.files.blocks.qmmm_blocks module pygromos.files.blocks.replica_exchange_blocks module pygromos.files.blocks.topology_blocks module pygromos.files.coord module pygromos.files.coord.cnf module pygromos.files.coord.posres module pygromos.files.coord.refpos module pygromos.files.forcefield module pygromos.files.forcefield.amber module pygromos.files.forcefield.amber.amberff module pygromos.files.forcefield.gromos module pygromos.files.forcefield.gromos.gromosff module pygromos.files.forcefield.openff module pygromos.files.forcefield.openff.openff module pygromos.files.forcefield.serenityff module pygromos.files.forcefield.serenityff.serenityff module pygromos.files.forcefield.serenityff.serenityff_data module pygromos.files.gromos_system module pygromos.files.gromos_system.gromos_system module pygromos.files.otherfiles module pygromos.files.otherfiles.new_repdat module pygromos.files.otherfiles.noe_output module pygromos.files.otherfiles.repdat module pygromos.files.otherfiles.residue_library module pygromos.files.qmmm module pygromos.files.qmmm.qmmm module pygromos.files.simulation_parameters module

pygromos.files.simulation_parameters.imd module pygromos.files.topology module pygromos.files.topology.disres module pygromos.files.topology.ifp module pygromos.files.topology.mtb module pygromos.files.topology.ptp module pygromos.files.topology.top module pygromos.files.trajectory module pygromos.files.trajectory.blocks module pygromos.files.trajectory.blocks.energy_trajectory_subblock module pygromos.files.trajectory.blocks.trajectory_blocks module pygromos.files.trajectory.trc module pygromos.files.trajectory.tre module pygromos.files.trajectory.tre_field_libs module pygromos.files.trajectory.tre_field_libs.ene_fields module pygromos.files.trajectory.trg module pygromos.gromos module pygromos.gromos.compile_gromos module pygromos.gromos.gromosBashSyntaxParser module pygromos.gromos.gromosPP module pygromos.gromos.gromosXX module pygromos.gromos.pyGromosPP module pygromos.gromos.pyGromosPP.com_top module pygromos.gromos.pyGromosPP.ran_box module pygromos.pygromos module pygromos.simulations module pygromos.simulations.approaches module pygromos.simulations.approaches.hvap_calculation module pygromos.simulations.approaches.hvap_calculation.hvap_calculation module pygromos.simulations.approaches.hvap_calculation.hvap_input_files module pygromos.simulations.hpc_queuing module pygromos.simulations.hpc_queuing.job_scheduling module pygromos.simulations.hpc_queuing.job_scheduling.file_management module pygromos.simulations.hpc_queuing.job_scheduling.module_functions module pygromos.simulations.hpc_queuing.job_scheduling.schedulers module pygromos.simulations.hpc_queuing.job_scheduling.schedulers.scheduler_functions module pygromos.simulations.hpc_queuing.job_scheduling.schedulers.simulation_scheduler module pygromos.simulations.hpc_queuing.job_scheduling.workers module pygromos.simulations.hpc_queuing.job_scheduling.workers.analysis_workers module pygromos.simulations.hpc_queuing.job_scheduling.workers.analysis_workers.simulation_analysis module pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers module pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.clean_up_simulation_files module pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.simulation_run_worker module pygromos.simulations.hpc_queuing.submission_systems module pygromos.simulations.hpc_queuing.submission_systems.dummy module pygromos.simulations.hpc_queuing.submission_systems.local module pygromos.simulations.hpc_queuing.submission_systems.lsf module pygromos.simulations.hpc_queuing.submission_systems.submission_job module pygromos.simulations.modules module pygromos.simulations.modules.general_analysis_modules module pygromos.simulations.modules.general_simulation_modules module pygromos.simulations.modules.preset_simulation_modules module pygromos.simulations.modules.ti_modules module pygromos.tests module pygromos.tests.in_testfiles module pygromos.tests.out_testresults module pygromos.tests.test_analysis module pygromos.tests.test_analysis.test_error_estimate module pygromos.tests.test_analysis.test_freeEnergy module pygromos.tests.test_approaches module pygromos.tests.test_approaches.test_solvation_free_ernergy module pygromos.tests.test_files module pygromos.tests.test_files.general_file_functions module pygromos.tests.test_files.test_cnf_funcs module pygromos.tests.test_files.test_disres module pygromos.tests.test_files.test_disres_file module pygromos.tests.test_files.test_gromosSystem module pygromos.tests.test_files.test_gromosSystem_forcefields module pygromos.tests.test_files.test_imd module pygromos.tests.test_files.test_imd_block module pygromos.tests.test_files.test_mtb module pygromos.tests.test_files.test_ptp module pygromos.tests.test_files.test_qmmm module pygromos.tests.test_files.test_repdat module pygromos.tests.test_files.test_resnlib module pygromos.tests.test_files.test_top module pygromos.tests.test_files.test_trajectory module pygromos.tests.test_pygromos module pygromos.tests.test_simulation_blocks module pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks module pygromos.tests.test_submission module pygromos.tests.test_submission.test_hpc_queuing_submission_job module pygromos.tests.test_submission.test_hpc_queuing_submission_scheduling module pygromos.tests.test_submission.test_hpc_queuing_submission_systems module pygromos.utils module pygromos.utils.amino_acids module pygromos.utils.bash module pygromos.utils.compiledProgram module pygromos.utils.pdb module pygromos.utils.typing module pygromos.utils.utils module pygromos.visualization module pygromos.visualization.coordinates_visualization module pyGromosWatermark (pygromos.files.blocks.pertubation_blocks.TITLE attribute)

Q

QMLJ (pygromos.files.blocks.imd_blocks.QMMM attribute) QMMM (class in pygromos.files.blocks.imd_blocks) (class in pygromos.files.qmmm.qmmm) qmmm (pygromos.files.gromos_system.gromos_system.Gromos_System property) QMMM (pygromos.files.simulation_parameters.imd.Imd attribute)

QMUNIT (class in pygromos.files.blocks.qmmm_blocks) (pygromos.files.qmmm.qmmm.QMMM attribute) QMZONE (class in pygromos.files.blocks.qmmm_blocks) (pygromos.files.qmmm.qmmm.QMMM attribute) qmzone_field (class in pygromos.files.blocks.qmmm_blocks) queue_after_jobID (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property)

R

ran_box() (in module pygromos.gromos.pyGromosPP.ran_box) (pygromos.gromos.gromosPP._gromosPPbase method) randomize_seed() (pygromos.files.simulation_parameters.imd.Imd method) RANDOMNUMBERS (class in pygromos.files.blocks.imd_blocks) RCRF (pygromos.files.blocks.imd_blocks.NONBONDED attribute) RCUTF (pygromos.files.blocks.imd_blocks.STOCHDYN attribute) RCUTL (pygromos.files.blocks.imd_blocks.PAIRLIST attribute) RCUTPL (pygromos.files.blocks.imd_blocks.PAIRLIST attribute) RCUTQ (pygromos.files.blocks.imd_blocks.QMMM attribute) rdkit2Gromos() (pygromos.files.gromos_system.gromos_system.Gromos_System method) rdkit2GromosName() (pygromos.files.gromos_system.gromos_system.Gromos_System method) rdkitImport() (pygromos.files.gromos_system.gromos_system.Gromos_System method) read_blocks() (pygromos.files.topology.disres.Distance_restraints method) (pygromos.files.topology.ptp.Pertubation_topology method) read_content_from_str() (pygromos.files.blocks.coord_blocks.GENBOX method) (pygromos.files.blocks.coord_blocks.LATTICESHIFTS method) (pygromos.files.blocks.coord_blocks.PERTDATA method) (pygromos.files.blocks.coord_blocks.POSITION method) (pygromos.files.blocks.coord_blocks.POSRESSPEC method) (pygromos.files.blocks.coord_blocks.REFPOSITION method) (pygromos.files.blocks.coord_blocks.STOCHINT method) (pygromos.files.blocks.coord_blocks.VELOCITY method) (pygromos.files.blocks.imd_blocks.EDS method) (pygromos.files.blocks.imd_blocks.FORCE method) (pygromos.files.blocks.imd_blocks.MULTIBATH method) (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS method) (pygromos.files.blocks.imd_blocks.PRESSURESCALE method) (pygromos.files.blocks.imd_blocks.REPLICA method) (pygromos.files.blocks.imd_blocks.REPLICA_EDS method) (pygromos.files.blocks.miscBlocks.ATOMNAMELIB method) (pygromos.files.blocks.miscBlocks.RESIDUENAMELIB method) (pygromos.files.blocks.mtb_blocks.LINKEXCLUSIONS method) (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND method) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE method) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLVENT method) (pygromos.files.blocks.pertubation_blocks.MPERTATOM method) (pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM method) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLE method) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLEH method) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCH method) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCHH method) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIH method) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIHH method) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIH method) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH method) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH.PERTPROPERDIH method) (pygromos.files.blocks.pertubation_blocks.TITLE method) (pygromos.files.blocks.qmmm_blocks.QMUNIT method) (pygromos.files.blocks.topology_blocks.BOND method) (pygromos.files.blocks.topology_blocks.BONDANGLE method) (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPE method) (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPECODE method) (pygromos.files.blocks.topology_blocks.BONDANGLEH method) (pygromos.files.blocks.topology_blocks.BONDH method) (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPE method) (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPECODE method) (pygromos.files.blocks.topology_blocks.CONSTRAINT method) (pygromos.files.blocks.topology_blocks.CROSSDIHEDRAL method) (pygromos.files.blocks.topology_blocks.CROSSDIHEDRALH method) (pygromos.files.blocks.topology_blocks.DIHEDRAL method) (pygromos.files.blocks.topology_blocks.DIHEDRALH method) (pygromos.files.blocks.topology_blocks.DISTANCERESSPEC method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRAL method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALH method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPE method) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPECODE method) (pygromos.files.blocks.topology_blocks.LJEXCEPTIONS method) (pygromos.files.blocks.topology_blocks.LJPARAMETERS method) (pygromos.files.blocks.topology_blocks.MASSATOMTYPECODE method) (pygromos.files.blocks.topology_blocks.MIXEDATOMLJPAIR method) (pygromos.files.blocks.topology_blocks.PERTATOMPARAM method) (pygromos.files.blocks.topology_blocks.PHYSICALCONSTANTS method) (pygromos.files.blocks.topology_blocks.SCALEDINTERACTIONS method) (pygromos.files.blocks.topology_blocks.SINGLEATOMLJPAIR method) (pygromos.files.blocks.topology_blocks.SOLUTEATOM method) (pygromos.files.blocks.topology_blocks.SOLVENTATOM method) (pygromos.files.blocks.topology_blocks.SOLVENTCONSTR method) (pygromos.files.blocks.topology_blocks.SPECATOMLJPAIR method) (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPE method) (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPECODE method) read_file() (pygromos.files.coord.cnf.Cnf method) (pygromos.files.otherfiles.noe_output.JVAL method) (pygromos.files.otherfiles.noe_output.NOE method) (pygromos.files.qmmm.qmmm.QMMM method) (pygromos.files.simulation_parameters.imd.Imd method) (pygromos.files.topology.ifp.Ifp method) (pygromos.files.topology.mtb.Mtb method) (pygromos.files.topology.top.Top method)

read_files() (pygromos.files.gromos_system.gromos_system.Gromos_System method) read_mtb_file() (pygromos.files.topology.mtb.Mtb method) read_pattern() (pygromos.files.forcefield.serenityff.serenityff.SerenityFF method) read_pdb_simple() (in module pygromos.utils.pdb) read_resnlib() (pygromos.files.otherfiles.residue_library.residue_library method) readBlock() (in module pygromos.data.ff.addAtomType) readFile() (in module pygromos.data.ff.addAtomType) real_atom (pygromos.files.blocks.topology_blocks.geometric_code attribute) rebase_files() (pygromos.files.gromos_system.gromos_system.Gromos_System method) recenter_pbc() (pygromos.files.coord.cnf.Cnf method) recreate_view() (pygromos.files.coord.cnf.Cnf method) (pygromos.files.trajectory.trc.Trc method) rectangular (pygromos.files.blocks.coord_blocks.Pbc attribute) red_top() (pygromos.gromos.gromosPP._gromosPPbase method) REEDS (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) (pygromos.files.blocks.imd_blocks.REPLICA_EDS attribute) Reference_Position (class in pygromos.files.coord.refpos) refpos (pygromos.files.gromos_system.gromos_system.Gromos_System property) REFPOSITION (class in pygromos.files.blocks.coord_blocks) (class in pygromos.files.trajectory.blocks.trajectory_blocks) (pygromos.files.coord.refpos.Reference_Position attribute) RELAM (pygromos.files.blocks.imd_blocks.REPLICA attribute) remove_file() (in module pygromos.utils.bash) remove_folder() (in module pygromos.utils.bash) rename_atom_attribute() (in module pygromos.utils.pdb) rename_atom_types() (in module pygromos.utils.pdb) rename_residue() (pygromos.files.coord.cnf.Cnf method) reorder_lines() (in module pygromos.utils.pdb) Repdat (class in pygromos.files.otherfiles.new_repdat) (class in pygromos.files.otherfiles.repdat) repex_run() (pygromos.gromos.gromosXX._GromosXX method) repex_system (class in pygromos.files.blocks.replica_exchange_blocks) replace_text_in_text_file() (in module pygromos.utils.bash) replacing_atoms (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND attribute) REPLICA (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) REPLICA_EDS (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) replica_round_trips (pygromos.files.otherfiles.new_repdat.Repdat attribute) (pygromos.files.otherfiles.repdat.Repdat attribute) replica_stat (class in pygromos.files.blocks.replica_exchange_blocks) required_blocks (pygromos.files.otherfiles.residue_library.residue_library attribute) (pygromos.files.topology.disres.Distance_restraints attribute) (pygromos.files.topology.ptp.Pertubation_topology attribute) required_files (pygromos.files.gromos_system.gromos_system.Gromos_System attribute) RES (pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS attribute) (pygromos.files.blocks.imd_blocks.REPLICA_EDS attribute) residue_library (class in pygromos.files.otherfiles.residue_library) residue_list (pygromos.files.gromos_system.gromos_system.Gromos_System attribute) RESIDUENAMELIB (class in pygromos.files.blocks.miscBlocks) (pygromos.files.otherfiles.residue_library.residue_library attribute) residues (pygromos.files.coord.cnf.Cnf attribute) (pygromos.files.coord.posres.Position_Restraints attribute) (pygromos.files.coord.refpos.Reference_Position attribute) RESNAME (class in pygromos.files.blocks.topology_blocks) RESTRAINT_LEGEND (pygromos.files.otherfiles.noe_output.NOE attribute) RET (pygromos.files.blocks.imd_blocks.REPLICA attribute) RETL (pygromos.files.blocks.imd_blocks.REPLICA attribute) RETS (pygromos.files.blocks.imd_blocks.REPLICA attribute) rgyr() (pygromos.gromos.gromosPP._gromosPPbase method) RLAM (pygromos.files.blocks.imd_blocks.PERTURBATION attribute) rms() (in module pygromos.analysis.coordinate_analysis) rmsd() (pygromos.files.trajectory.trc.Trc method) (pygromos.gromos.gromosPP._gromosPPbase method) rmsf() (pygromos.gromos.gromosPP._gromosPPbase method) root_out (pygromos.tests.test_files.test_cnf_funcs.test_cnf attribute) (pygromos.tests.test_files.test_disres.test_disres attribute) (pygromos.tests.test_files.test_disres_file.test_disres attribute) (pygromos.tests.test_files.test_imd.test_imd attribute) (pygromos.tests.test_files.test_mtb.test_mtb attribute) (pygromos.tests.test_files.test_ptp.test_ptp attribute) (pygromos.tests.test_files.test_qmmm.test_qmmm attribute) (pygromos.tests.test_files.test_qmmm.test_qmmm_imd attribute) (pygromos.tests.test_files.test_repdat.test_repdat attribute) (pygromos.tests.test_files.test_resnlib.test_resnlib attribute) (pygromos.tests.test_files.test_top.test_top attribute) (pygromos.tests.test_files.test_top.test_top_simple attribute) rotate() (pygromos.files.coord.cnf.Cnf method) ROTTRANS (class in pygromos.files.blocks.imd_blocks) RTC (pygromos.files.blocks.imd_blocks.ROTTRANS attribute) RTCLAST (pygromos.files.blocks.imd_blocks.ROTTRANS attribute) run (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) run() (pygromos.simulations.approaches.hvap_calculation.hvap_calculation.Hvap_calculation method) run_gas() (pygromos.simulations.approaches.hvap_calculation.hvap_calculation.Hvap_calculation method) run_liq() (pygromos.simulations.approaches.hvap_calculation.hvap_calculation.Hvap_calculation method)

S

s (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) sasa() (pygromos.gromos.gromosPP._gromosPPbase method) save() (pygromos.files.gromos_system.gromos_system.Gromos_System method) (pygromos.files.trajectory.trc.Trc method) save_make_folder() (in module pygromos.utils.bash) SCALE (pygromos.files.blocks.imd_blocks.PRESSURESCALE attribute) SCALEDINTERACTIONS (class in pygromos.files.blocks.topology_blocks) sd() (in module pygromos.simulations.modules.preset_simulation_modules) search_queue_for_jobid() (pygromos.simulations.hpc_queuing.submission_systems.local.LOCAL method) (pygromos.simulations.hpc_queuing.submission_systems.lsf.LSF method) search_queue_for_jobname() (pygromos.simulations.hpc_queuing.submission_systems.dummy.DUMMY method) (pygromos.simulations.hpc_queuing.submission_systems.local.LOCAL method) (pygromos.simulations.hpc_queuing.submission_systems.lsf.LSF method) SEMIANISOTROPIC (pygromos.files.blocks.imd_blocks.PRESSURESCALE attribute) SerenityFF (class in pygromos.files.forcefield.serenityff.serenityff) set_parameters() (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio method) (pygromos.analysis.free_energy_calculation.zwanzigEquation method) setUp() (pygromos.tests.test_files.test_gromosSystem.test_gromos_system method) (pygromos.tests.test_files.test_trajectory.traj_standard_tests method) (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks method) (pygromos.tests.test_submission.test_hpc_queuing_submission_scheduling.test_MD_scheduler method) sf (pygromos.tests.test_approaches.test_solvation_free_ernergy.test_sfe attribute) SHAKEFAILPOSITION (class in pygromos.files.trajectory.blocks.trajectory_blocks) SHAKEFAILPREVPOSITION (class in pygromos.files.trajectory.blocks.trajectory_blocks) shift_periodic_boundary() (pygromos.files.coord.cnf.Cnf method) si (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) sim_block() (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks method) sim_box() (pygromos.gromos.gromosPP._gromosPPbase method) simulation() (in module pygromos.simulations.modules.general_simulation_modules) single_atom_lj_pair_type (class in pygromos.files.blocks.topology_blocks) SINGLEATOMLJPAIR (class in pygromos.files.blocks.topology_blocks) SIZE (pygromos.files.blocks.imd_blocks.PAIRLIST attribute) sj (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) skip_lines (pygromos.files.blocks.mtb_blocks.MTBUILDBLEND attribute) (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE attribute) SLVDNS (pygromos.files.blocks.imd_blocks.NONBONDED attribute) smiles (pygromos.tests.test_approaches.test_solvation_free_ernergy.test_sfe attribute) (pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_forcefields attribute) solute_info (pygromos.files.gromos_system.gromos_system.Gromos_System attribute) solute_infos (in module pygromos.files.coord.cnf) SOLUTEATOM (class in pygromos.files.blocks.topology_blocks) soluteatom_type (class in pygromos.files.blocks.topology_blocks) SOLUTEMOLECULES (class in pygromos.files.blocks.topology_blocks) solvate (pygromos.files.forcefield.amber.amberff.AmberFF attribute) solvent_info (pygromos.files.gromos_system.gromos_system.Gromos_System attribute) solvent_infos (in module pygromos.files.coord.cnf) SOLVENTATOM (class in pygromos.files.blocks.topology_blocks) solventatom_type (class in pygromos.files.blocks.topology_blocks) solventbox (pygromos.files.forcefield.amber.amberff.AmberFF attribute) SOLVENTCONSTR (class in pygromos.files.blocks.topology_blocks)

solventconstr_type (class in pygromos.files.blocks.topology_blocks) SPECATOMLJPAIR (class in pygromos.files.blocks.topology_blocks) special (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) special_atom_lj_pair_type (class in pygromos.files.blocks.topology_blocks) start_job (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property) state_format_pattern (pygromos.files.blocks.pertubation_blocks.atom_eds_pertubation_state attribute) (pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state attribute) (pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_angle attribute) (pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_bond attribute) (pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_dihedral attribute) (pygromos.files.blocks.topology_blocks.atom_lam_pertubation_state attribute) state_potentials (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) states (pygromos.files.blocks.pertubation_blocks.MPERTATOM property) (pygromos.files.blocks.pertubation_blocks.PERTATOMPARAM property) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLE property) (pygromos.files.blocks.pertubation_blocks.PERTBONDANGLEH property) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCH property) (pygromos.files.blocks.pertubation_blocks.PERTBONDSTRETCHH property) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIH property) (pygromos.files.blocks.pertubation_blocks.PERTIMROPERDIHH property) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIH property) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH property) (pygromos.files.blocks.pertubation_blocks.PERTPROPERDIHH.PERTPROPERDIH property) (pygromos.files.blocks.topology_blocks.PERTATOMPARAM property) STEP (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute) step (pygromos.files.trajectory.trc.Trc property) STOCHDYN (class in pygromos.files.blocks.imd_blocks) STOCHINT (class in pygromos.files.blocks.coord_blocks) str2bool() (in module pygromos.utils.utils) submission (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_LOCAL attribute) (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_LSF attribute) (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_queuing_system attribute) Submission_job (class in pygromos.simulations.hpc_queuing.submission_systems.submission_job) submissionSystem (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks attribute) (pygromos.tests.test_submission.test_hpc_queuing_submission_scheduling.test_MD_scheduler attribute) submissonSystem_gas (pygromos.simulations.approaches.hvap_calculation.hvap_calculation.Hvap_calculation attribute) submissonSystem_liq (pygromos.simulations.approaches.hvap_calculation.hvap_calculation.Hvap_calculation attribute) submit_from_dir (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property) submit_jobAarray_to_queue() (pygromos.simulations.hpc_queuing.submission_systems.dummy.DUMMY method) (pygromos.simulations.hpc_queuing.submission_systems.local.LOCAL method) (pygromos.simulations.hpc_queuing.submission_systems.lsf.LSF method) submit_to_queue() (pygromos.simulations.hpc_queuing.submission_systems.dummy.DUMMY method) (pygromos.simulations.hpc_queuing.submission_systems.local.LOCAL method) (pygromos.simulations.hpc_queuing.submission_systems.lsf.LSF method) sumbit_from_file (pygromos.simulations.hpc_queuing.submission_systems.submission_job.Submission_job property) supress_atomPosition_singulrarities() (pygromos.files.coord.cnf.Cnf method) SYSTEM (class in pygromos.files.blocks.imd_blocks) (pygromos.files.otherfiles.new_repdat.Repdat attribute) (pygromos.files.otherfiles.repdat.Repdat attribute) (pygromos.files.simulation_parameters.imd.Imd attribute)

T

T (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) (pygromos.analysis.free_energy_calculation.threeStateZwanzig attribute) (pygromos.analysis.free_energy_calculation.zwanzigEquation attribute) (pygromos.files.blocks.imd_blocks.STEP attribute) table_header (pygromos.files.blocks.qmmm_blocks.QMUNIT attribute) (pygromos.files.blocks.qmmm_blocks.QMZONE attribute) (pygromos.files.blocks.topology_blocks.BOND attribute) (pygromos.files.blocks.topology_blocks.BONDANGLE attribute) (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPE attribute) (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPECODE attribute) (pygromos.files.blocks.topology_blocks.BONDANGLEH attribute) (pygromos.files.blocks.topology_blocks.BONDH attribute) (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPE attribute) (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPECODE attribute) (pygromos.files.blocks.topology_blocks.CONSTRAINT attribute) (pygromos.files.blocks.topology_blocks.CROSSDIHEDRAL attribute) (pygromos.files.blocks.topology_blocks.CROSSDIHEDRALH attribute) (pygromos.files.blocks.topology_blocks.DIHEDRAL attribute) (pygromos.files.blocks.topology_blocks.DIHEDRALH attribute) (pygromos.files.blocks.topology_blocks.IMPDIHEDRAL attribute) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALH attribute) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPE attribute) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPECODE attribute) (pygromos.files.blocks.topology_blocks.LJEXCEPTIONS attribute) (pygromos.files.blocks.topology_blocks.LJPARAMETERS attribute) (pygromos.files.blocks.topology_blocks.MASSATOMTYPECODE attribute) (pygromos.files.blocks.topology_blocks.MIXEDATOMLJPAIR attribute) (pygromos.files.blocks.topology_blocks.SINGLEATOMLJPAIR attribute) (pygromos.files.blocks.topology_blocks.SOLUTEATOM attribute) (pygromos.files.blocks.topology_blocks.SOLVENTATOM attribute) (pygromos.files.blocks.topology_blocks.SOLVENTCONSTR attribute) (pygromos.files.blocks.topology_blocks.SPECATOMLJPAIR attribute) (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPE attribute) (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPECODE attribute) table_line_type (pygromos.files.blocks.qmmm_blocks.QMZONE attribute) (pygromos.files.blocks.topology_blocks.BOND attribute) (pygromos.files.blocks.topology_blocks.BONDANGLE attribute) (pygromos.files.blocks.topology_blocks.BONDANGLEBENDTYPE attribute) (pygromos.files.blocks.topology_blocks.BONDANGLEH attribute) (pygromos.files.blocks.topology_blocks.BONDH attribute) (pygromos.files.blocks.topology_blocks.BONDSTRETCHTYPE attribute) (pygromos.files.blocks.topology_blocks.CONSTRAINT attribute) (pygromos.files.blocks.topology_blocks.CROSSDIHEDRAL attribute) (pygromos.files.blocks.topology_blocks.CROSSDIHEDRALH attribute) (pygromos.files.blocks.topology_blocks.DIHEDRAL attribute) (pygromos.files.blocks.topology_blocks.DIHEDRALH attribute) (pygromos.files.blocks.topology_blocks.IMPDIHEDRAL attribute) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALH attribute) (pygromos.files.blocks.topology_blocks.IMPDIHEDRALTYPE attribute) (pygromos.files.blocks.topology_blocks.LJEXCEPTIONS attribute) (pygromos.files.blocks.topology_blocks.LJPARAMETERS attribute) (pygromos.files.blocks.topology_blocks.SOLVENTATOM attribute) (pygromos.files.blocks.topology_blocks.SOLVENTCONSTR attribute) (pygromos.files.blocks.topology_blocks.TORSDIHEDRALTYPE attribute) TAU (pygromos.files.blocks.imd_blocks.MULTIBATH attribute) TAUDIR (pygromos.files.blocks.imd_blocks.DISTANCERES attribute) TAUP (pygromos.files.blocks.imd_blocks.PRESSURESCALE attribute) TEMP0 (pygromos.files.blocks.imd_blocks.MULTIBATH attribute) temperature (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) TEMPERATUREGROUPS (class in pygromos.files.blocks.topology_blocks) TEMPI (pygromos.files.blocks.imd_blocks.INITIALISE attribute) TEMPSD (pygromos.files.blocks.imd_blocks.STOCHDYN attribute) test_acces() (pygromos.tests.test_submission.test_hpc_queuing_submission_job.test_queuing_system method) test_add() (pygromos.tests.test_files.test_trajectory.traj_standard_tests method) test_add_eds_state() (pygromos.tests.test_files.test_ptp.test_ptp method) test_add_eq_mul() (pygromos.tests.test_files.test_top.test_top_simple method) test_additon() (pygromos.tests.test_files.test_top.test_top_simple method) test_all_mtb_solutes_read() (pygromos.tests.test_files.test_mtb.test_mtb_orga method) test_array (pygromos.tests.test_analysis.test_error_estimate.test_ee attribute) test_BAR (class in pygromos.tests.test_analysis.test_freeEnergy) test_box_generation() (pygromos.tests.test_approaches.test_solvation_free_ernergy.test_sfe method) test_CHE_read() (pygromos.tests.test_files.test_mtb.test_mtb_orga method) test_clean_posiResNumsByName() (pygromos.tests.test_files.test_cnf_funcs.test_cnf method) test_cleaning_concat() (pygromos.tests.test_files.test_repdat.test_repdat method) test_cnf (class in pygromos.tests.test_files.test_cnf_funcs) test_construct() (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_queuing_system method) test_construct_empty() (pygromos.tests.test_files.test_gromosSystem.test_gromos_system method) (pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_forcefields method) test_construct_files() (pygromos.tests.test_files.test_gromosSystem.test_gromos_system method) test_construct_full() (pygromos.tests.test_submission.test_hpc_queuing_submission_job.test_queuing_system method) test_construct_min() (pygromos.tests.test_submission.test_hpc_queuing_submission_job.test_queuing_system method) test_construct_top_from_ff() (pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_forcefields method) test_constructor() (pygromos.tests.test_analysis.test_error_estimate.test_ee method) (pygromos.tests.test_analysis.test_freeEnergy.test_ZwanzigEquation method) (pygromos.tests.test_approaches.test_solvation_free_ernergy.test_sfe method) test_constructor_empty() (pygromos.tests.test_files.test_trajectory.test_trc method) (pygromos.tests.test_files.test_trajectory.traj_standard_tests method) test_constructor_trc_file_noTop_path() (pygromos.tests.test_files.test_trajectory.test_trc method) test_constructor_trc_file_path() (pygromos.tests.test_files.test_trajectory.test_trc method) test_constructor_trc_h5_file_path() (pygromos.tests.test_files.test_trajectory.test_trc method) test_constructor_trg_file_path() (pygromos.tests.test_files.test_trajectory.traj_standard_tests method) test_constructor_trg_h5_file_path() (pygromos.tests.test_files.test_trajectory.traj_standard_tests method) test_copy() (pygromos.tests.test_files.general_file_functions.general_file_tests method) test_deepcopy() (pygromos.tests.test_files.general_file_functions.general_file_tests method) test_delete_eds_state() (pygromos.tests.test_files.test_ptp.test_ptp method) test_delete_res() (pygromos.tests.test_files.test_cnf_funcs.test_cnf method) test_disres (class in pygromos.tests.test_files.test_disres) (class in pygromos.tests.test_files.test_disres_file) test_do() (pygromos.tests.test_submission.test_hpc_queuing_submission_scheduling.test_MD_scheduler method) test_DUMMY (class in pygromos.tests.test_submission.test_hpc_queuing_submission_systems) test_edit_REEDS() (pygromos.tests.test_files.test_imd.test_imd method) test_eds_gen_all_states_ptp() (pygromos.tests.test_files.test_ptp.test_ptp method) test_ee (class in pygromos.tests.test_analysis.test_error_estimate) test_emin() (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks method) test_energy_groups() (pygromos.tests.test_approaches.test_solvation_free_ernergy.test_sfe method) test_eq_imd() (pygromos.tests.test_approaches.test_solvation_free_ernergy.test_sfe method) test_equalAfterCopy() (pygromos.tests.test_files.general_file_functions.general_file_tests method) test_equality() (pygromos.tests.test_files.general_file_functions.general_file_tests method) test_error_estimate() (pygromos.tests.test_analysis.test_error_estimate.test_ee method) test_free_Energy1() (pygromos.tests.test_analysis.test_freeEnergy.test_BAR method) (pygromos.tests.test_analysis.test_freeEnergy.test_threeStateZwanzigReweighting method) (pygromos.tests.test_analysis.test_freeEnergy.test_ZwanzigEquation method) test_get_eds() (pygromos.tests.test_files.test_trajectory.test_tre method) test_get_eds_states() (pygromos.tests.test_files.test_ptp.test_ptp method) test_get_jobs_from_queue() (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_queuing_system method) test_get_lam() (pygromos.tests.test_files.test_trajectory.test_tre method) test_get_lambdas() (pygromos.tests.test_files.test_trajectory.test_trg method) test_get_precalclam() (pygromos.tests.test_files.test_trajectory.test_trg method) test_get_totals() (pygromos.tests.test_files.test_trajectory.test_tre method) (pygromos.tests.test_files.test_trajectory.test_trg method) test_get_transitions() (pygromos.tests.test_files.test_repdat.test_repdat method) test_gromos_system (class in pygromos.tests.test_files.test_gromosSystem) test_gromos_system_2016H66 (class in pygromos.tests.test_files.test_gromosSystem_forcefields) test_gromos_system_54A7 (class in pygromos.tests.test_files.test_gromosSystem_forcefields) test_gromos_system_forcefields (class in pygromos.tests.test_files.test_gromosSystem_forcefields) test_imd (class in pygromos.tests.test_files.test_imd) test_imd_block (class in pygromos.tests.test_files.test_imd_block) test_IO() (pygromos.tests.test_files.test_ptp.test_ptp method) (pygromos.tests.test_files.test_resnlib.test_resnlib method) test_lam_window() (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks method) test_load() (pygromos.tests.test_files.test_gromosSystem.test_gromos_system method) test_LOCAL (class in pygromos.tests.test_submission.test_hpc_queuing_submission_systems) test_LSF (class in pygromos.tests.test_submission.test_hpc_queuing_submission_systems) test_md() (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks method) test_MD_scheduler (class in pygromos.tests.test_submission.test_hpc_queuing_submission_scheduling) test_min_imd() (pygromos.tests.test_approaches.test_solvation_free_ernergy.test_sfe method) test_mtb (class in pygromos.tests.test_files.test_mtb) test_mtb_g54a7 (class in pygromos.tests.test_files.test_mtb) test_mtb_orga (class in pygromos.tests.test_files.test_mtb) test_multiplication() (pygromos.tests.test_files.test_top.test_top_simple method) test_new_eds_ptp_from_scratch() (pygromos.tests.test_files.test_ptp.test_ptp method) test_parse() (pygromos.tests.test_files.test_cnf_funcs.test_cnf method) test_parsing_new_file() (pygromos.tests.test_files.test_repdat.test_repdat method) test_parsing_test_file() (pygromos.tests.test_files.test_disres.test_disres method) (pygromos.tests.test_files.test_disres_file.test_disres method) (pygromos.tests.test_files.test_imd.test_imd method) (pygromos.tests.test_files.test_mtb.test_mtb method) (pygromos.tests.test_files.test_qmmm.test_qmmm method) (pygromos.tests.test_files.test_qmmm.test_qmmm_imd method) (pygromos.tests.test_files.test_repdat.test_repdat method) (pygromos.tests.test_files.test_top.test_top method) (pygromos.tests.test_files.test_top.test_top_simple method) test_pickle() (pygromos.tests.test_files.general_file_functions.general_file_tests method) test_ptp (class in pygromos.tests.test_files.test_ptp) test_ptp_file() (pygromos.tests.test_approaches.test_solvation_free_ernergy.test_sfe method) test_pygromos_imported() (in module pygromos.tests.test_pygromos) test_qmmm (class in pygromos.tests.test_files.test_qmmm) test_qmmm_imd (class in pygromos.tests.test_files.test_qmmm) test_queuing_system (class in pygromos.tests.test_submission.test_hpc_queuing_submission_job) (class in pygromos.tests.test_submission.test_hpc_queuing_submission_systems) test_rebase() (pygromos.tests.test_files.test_gromosSystem.test_gromos_system method) test_remove_eds_atoms() (pygromos.tests.test_files.test_ptp.test_ptp method) test_repdat (class in pygromos.tests.test_files.test_repdat)

test_resnlib (class in pygromos.tests.test_files.test_resnlib) test_sd() (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks method) test_search_queue_for_jobname() (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_queuing_system method) test_sfe (class in pygromos.tests.test_approaches.test_solvation_free_ernergy) test_simulation_blocks (class in pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks) test_smulation() (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks method) test_some_blocks() (pygromos.tests.test_files.test_imd_block.test_imd_block method) test_submit() (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_queuing_system method) test_submit_jobAarray_to_queue() (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_queuing_system method) test_submit_jobAarray_to_queue1_10() (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_queuing_system method) test_test_transitions() (pygromos.tests.test_files.test_repdat.test_repdat method) test_threeStateZwanzigReweighting (class in pygromos.tests.test_analysis.test_freeEnergy) test_ti_imd() (pygromos.tests.test_approaches.test_solvation_free_ernergy.test_sfe method) test_ti_sampling() (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks method) test_to_conf() (pygromos.tests.test_files.test_trajectory.test_trc method) test_to_string() (pygromos.tests.test_files.test_imd.test_imd method) (pygromos.tests.test_files.test_qmmm.test_qmmm method) (pygromos.tests.test_files.test_qmmm.test_qmmm_imd method) test_to_trc_file() (pygromos.tests.test_files.test_trajectory.test_trc method) test_top (class in pygromos.tests.test_files.test_top) test_top_simple (class in pygromos.tests.test_files.test_top) test_trc (class in pygromos.tests.test_files.test_trajectory) test_trc_with_boxes_traj() (pygromos.tests.test_files.test_trajectory.test_trc method) test_tre (class in pygromos.tests.test_files.test_trajectory) test_trg (class in pygromos.tests.test_files.test_trajectory) test_visualize() (pygromos.tests.test_files.test_cnf_funcs.test_cnf method) test_write() (pygromos.tests.test_files.test_gromosSystem.test_gromos_system method) (pygromos.tests.test_files.test_mtb.test_mtb method) (pygromos.tests.test_files.test_trajectory.test_trc method) (pygromos.tests.test_files.test_trajectory.traj_standard_tests method) test_write_out() (pygromos.tests.test_files.test_cnf_funcs.test_cnf method) (pygromos.tests.test_files.test_imd.test_imd method) (pygromos.tests.test_files.test_qmmm.test_qmmm method) (pygromos.tests.test_files.test_qmmm.test_qmmm_imd method) (pygromos.tests.test_files.test_repdat.test_repdat method) test_ZwanzigEquation (class in pygromos.tests.test_analysis.test_freeEnergy) thread_worker_concat_repdat() (in module pygromos.simulations.hpc_queuing.job_scheduling.file_management) thread_worker_isolate_energies() (in module pygromos.simulations.hpc_queuing.job_scheduling.file_management) threeLetter (pygromos.utils.amino_acids.amino_acid attribute) threeStateZwanzig (class in pygromos.analysis.free_energy_calculation) Ti (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) TI_sampling() (in module pygromos.simulations.modules.ti_modules) TIMESTEP (class in pygromos.files.trajectory.blocks.trajectory_blocks) (pygromos.files.coord.cnf.Cnf attribute) TITLE (class in pygromos.files.blocks.pertubation_blocks) (pygromos.files.coord.cnf.Cnf attribute) (pygromos.files.coord.posres.Position_Restraints attribute) (pygromos.files.coord.refpos.Reference_Position attribute) (pygromos.files.otherfiles.noe_output.NOE attribute) (pygromos.files.qmmm.qmmm.QMMM attribute) (pygromos.files.simulation_parameters.imd.Imd attribute) (pygromos.files.topology.ptp.Pertubation_topology attribute) (pygromos.files.topology.ptp.Ptp attribute) (pygromos.files.trajectory.trc.Trc attribute) Tj (pygromos.files.blocks.replica_exchange_blocks.replica_stat attribute) tleap() (pygromos.files.forcefield.amber.amberff.amber2gromos method) to_cnf() (pygromos.files.trajectory.trc.Trc method) to_dict() (pygromos.files.trajectory.blocks.energy_trajectory_subblock.baths method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.bonded method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.eds method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.lam method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.mass method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.nonbonded method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.precalclam method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.pressure method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.special method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.temperature method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.totals method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.volume method) (pygromos.files.trajectory.blocks.energy_trajectory_subblock.xxx_copy_xxx method) (pygromos.files.trajectory.blocks.trajectory_blocks.ENERGY03 method) (pygromos.files.trajectory.blocks.trajectory_blocks.FREEENERDERIVS03 method) (pygromos.files.trajectory.blocks.trajectory_blocks.GENBOX method) (pygromos.files.trajectory.blocks.trajectory_blocks.POSITIONRED method) (pygromos.files.trajectory.blocks.trajectory_blocks.REFPOSITION method) (pygromos.files.trajectory.blocks.trajectory_blocks.SHAKEFAILPOSITION method) (pygromos.files.trajectory.blocks.trajectory_blocks.SHAKEFAILPREVPOSITION method) (pygromos.files.trajectory.blocks.trajectory_blocks.TIMESTEP method) (pygromos.files.trajectory.blocks.trajectory_blocks.VOLUMEPRESSURE03 method) to_string() (pygromos.files.blocks.coord_blocks.atomP method) (pygromos.files.blocks.coord_blocks.atomSI method) (pygromos.files.blocks.coord_blocks.atomV method) (pygromos.files.blocks.coord_blocks.lattice_shift method) (pygromos.files.blocks.mtb_blocks.mtb_angles_field method) (pygromos.files.blocks.mtb_blocks.mtb_atoms_field method) (pygromos.files.blocks.mtb_blocks.mtb_atoms_solvent_field method) (pygromos.files.blocks.mtb_blocks.mtb_bonds_field method) (pygromos.files.blocks.mtb_blocks.mtb_constraints_field method) (pygromos.files.blocks.mtb_blocks.mtb_dihedral_field method) (pygromos.files.blocks.mtb_blocks.mtb_lj_exceptions_field method) (pygromos.files.blocks.mtb_blocks.mtb_preceding_exclusions_field method) (pygromos.files.blocks.mtb_blocks.mtb_trailing_atoms_field method) (pygromos.files.blocks.pertubation_blocks.atom_eds_pertubation_state method) (pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state method) (pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_angle method) (pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_bond method) (pygromos.files.blocks.pertubation_blocks.atom_lam_pertubation_state_dihedral method) (pygromos.files.blocks.pertubation_blocks.atom_mass_type method) (pygromos.files.blocks.qmmm_blocks.qmzone_field method) (pygromos.files.blocks.replica_exchange_blocks.replica_stat method) (pygromos.files.blocks.topology_blocks.angle_type method) (pygromos.files.blocks.topology_blocks.atom_lam_pertubation_state method) (pygromos.files.blocks.topology_blocks.atom_mass_type method) (pygromos.files.blocks.topology_blocks.atom_pair_distanceRes method) (pygromos.files.blocks.topology_blocks.bond_type method) (pygromos.files.blocks.topology_blocks.bondangle_type method) (pygromos.files.blocks.topology_blocks.bondanglebendtype_type method) (pygromos.files.blocks.topology_blocks.bondstretchtype_type method) (pygromos.files.blocks.topology_blocks.constraint_type method) (pygromos.files.blocks.topology_blocks.crossgihedral_type method) (pygromos.files.blocks.topology_blocks.crossgihedralh_type method) (pygromos.files.blocks.topology_blocks.dihedral_type method) (pygromos.files.blocks.topology_blocks.dihedralh_type method) (pygromos.files.blocks.topology_blocks.impdihedral_type method) (pygromos.files.blocks.topology_blocks.impdihedralh_type method) (pygromos.files.blocks.topology_blocks.impdihedraltype_type method) (pygromos.files.blocks.topology_blocks.improper_dihedral_type method) (pygromos.files.blocks.topology_blocks.ljexception_type method) (pygromos.files.blocks.topology_blocks.ljparameters_type method) (pygromos.files.blocks.topology_blocks.mixed_atom_lj_pair_type method) (pygromos.files.blocks.topology_blocks.single_atom_lj_pair_type method) (pygromos.files.blocks.topology_blocks.soluteatom_type method) (pygromos.files.blocks.topology_blocks.solventatom_type method) (pygromos.files.blocks.topology_blocks.solventconstr_type method) (pygromos.files.blocks.topology_blocks.special_atom_lj_pair_type method) (pygromos.files.blocks.topology_blocks.top_bond_type method) (pygromos.files.blocks.topology_blocks.top_dihedral_type method) (pygromos.files.blocks.topology_blocks.torsdihedraltype_type method) TOLA2 (pygromos.files.blocks.imd_blocks.NONBONDED attribute) Top (class in pygromos.files.topology.top) top (pygromos.files.gromos_system.gromos_system.Gromos_System property) top_bond_type (class in pygromos.files.blocks.topology_blocks) top_dihedral_type (class in pygromos.files.blocks.topology_blocks) top_residue_list (pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_2016H66 attribute) (pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_54A7 attribute) (pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_forcefields attribute) TOPVERSION (class in pygromos.files.blocks.topology_blocks) TORSDIHEDRALTYPE (class in pygromos.files.blocks.topology_blocks) torsdihedraltype_type (class in pygromos.files.blocks.topology_blocks) TORSDIHEDRALTYPECODE (class in pygromos.files.blocks.topology_blocks) totals (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) totals_subblock_names (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2015_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2020_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_2021_tre_block_names_table attribute) (pygromos.files.trajectory.tre_field_libs.ene_fields.gromos_tre_block_names_table attribute) (pygromos.files.trajectory.trg.gromos_2020_trg_block_names_table attribute) trailing_atoms (pygromos.files.blocks.mtb_blocks.MTBUILDBLSOLUTE attribute) traj_files (pygromos.files.gromos_system.gromos_system.Gromos_System attribute) traj_standard_tests (class in pygromos.tests.test_files.test_trajectory) transition_traces (pygromos.files.otherfiles.new_repdat.Repdat attribute) (pygromos.files.otherfiles.repdat.Repdat attribute) Trc (class in pygromos.files.trajectory.trc) trc (pygromos.files.gromos_system.gromos_system.Gromos_System property) trc_outpath (pygromos.tests.test_files.test_trajectory.test_trc attribute) Tre (class in pygromos.files.trajectory.tre) tre (pygromos.files.gromos_system.gromos_system.Gromos_System property) Trg (class in pygromos.files.trajectory.trg) triclinic (pygromos.files.blocks.coord_blocks.Pbc attribute) trunc_octahedron (pygromos.files.blocks.coord_blocks.Pbc attribute) tser() (pygromos.gromos.gromosPP._gromosPPbase method) TURBOMOLEELEMENTS (class in pygromos.files.blocks.qmmm_blocks) (pygromos.files.qmmm.qmmm.QMMM attribute) TYPE (pygromos.files.blocks.imd_blocks.PAIRLIST attribute)

V

vacuum (pygromos.files.blocks.coord_blocks.Pbc attribute) VDIR (pygromos.files.blocks.imd_blocks.DISTANCERES attribute) VDW (pygromos.files.blocks.imd_blocks.FORCE attribute) VELOCITY (class in pygromos.files.blocks.coord_blocks) (pygromos.files.coord.cnf.Cnf attribute) verbose (pygromos.files.otherfiles.residue_library.residue_library attribute) (pygromos.simulations.hpc_queuing.submission_systems.dummy.DUMMY attribute) (pygromos.simulations.hpc_queuing.submission_systems.local.LOCAL attribute) (pygromos.tests.test_files.test_gromosSystem.test_gromos_system attribute) (pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_forcefields attribute) (pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks.test_simulation_blocks attribute) (pygromos.tests.test_submission.test_hpc_queuing_submission_systems.test_queuing_system attribute) VERSION (pygromos.files.blocks.topology_blocks.MAKETOPVERSION attribute) Vi (pygromos.analysis.free_energy_calculation.threeStateZwanzig attribute) (pygromos.analysis.free_energy_calculation.zwanzigEquation attribute) Vi_i (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) Vi_j (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute)

view (pygromos.files.coord.cnf.Cnf property) (pygromos.files.trajectory.trc.Trc property) VIRIAL (pygromos.files.blocks.imd_blocks.PRESSURESCALE attribute) virtual_atoms_cog (pygromos.files.blocks.topology_blocks.geometric_code attribute) virtual_atoms_com (pygromos.files.blocks.topology_blocks.geometric_code attribute) virtual_H_atom_aliphaticC (pygromos.files.blocks.topology_blocks.geometric_code attribute) virtual_H_atom_aliphaticC_strange (pygromos.files.blocks.topology_blocks.geometric_code attribute) virtual_H_atom_aromaticC (pygromos.files.blocks.topology_blocks.geometric_code attribute) virtual_H_atoms_goc_aliph (pygromos.files.blocks.topology_blocks.geometric_code attribute) visualize_system() (in module pygromos.visualization.coordinates_visualization) Vj (pygromos.analysis.free_energy_calculation.threeStateZwanzig attribute) (pygromos.analysis.free_energy_calculation.zwanzigEquation attribute) Vj_i (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) Vj_j (pygromos.analysis.free_energy_calculation.bennetAcceptanceRatio attribute) volume (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock) VOLUMEPRESSURE03 (class in pygromos.files.trajectory.blocks.trajectory_blocks) Vr (pygromos.analysis.free_energy_calculation.threeStateZwanzig attribute)

W

wait_for_fileSystem() (in module pygromos.utils.bash) which() (in module pygromos.utils.bash) work() (in module pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.simulation_run_worker) work_folder (pygromos.files.gromos_system.gromos_system.Gromos_System property) work_folder_no_update() (pygromos.files.gromos_system.gromos_system.Gromos_System method) workfolder (pygromos.tests.test_approaches.test_solvation_free_ernergy.test_sfe attribute) write() (pygromos.files.otherfiles.new_repdat.Repdat method) (pygromos.files.otherfiles.noe_output.JVAL method) (pygromos.files.otherfiles.repdat.Repdat method) (pygromos.files.trajectory.trc.Trc method) write_files() (pygromos.files.gromos_system.gromos_system.Gromos_System method) write_job_script() (in module pygromos.simulations.hpc_queuing.job_scheduling.module_functions) (in module pygromos.utils.utils)

write_json() (pygromos.files.simulation_parameters.imd.Imd method) write_pdb() (pygromos.files.coord.cnf.Cnf method) write_possrespec() (pygromos.files.coord.cnf.Cnf method) write_refpos() (pygromos.files.coord.cnf.Cnf method) write_trc() (pygromos.files.trajectory.trc.Trc method) write_xyz() (pygromos.files.coord.cnf.Cnf method) writeAtomTypes() (in module pygromos.data.ff.addAtomType) writeLine() (in module pygromos.data.ff.addAtomType) writeOut() (in module pygromos.data.ff.addAtomType) WRITETRAJ (class in pygromos.files.blocks.imd_blocks) (pygromos.files.simulation_parameters.imd.Imd attribute)

X

XTBELEMENTS (class in pygromos.files.blocks.qmmm_blocks) (pygromos.files.qmmm.qmmm.QMMM attribute)

xxx_copy_xxx (class in pygromos.files.trajectory.blocks.energy_trajectory_subblock)

Z

zwanzig (class in pygromos.analysis.free_energy_calculation)

zwanzigEquation (class in pygromos.analysis.free_energy_calculation)