Index A | B | C | D | E | F | G | I | L | M | N | O | P | R | S | T | U | V A acemd() (in module acemd.acemd) acemd.acemd module acemd.charmm module acemd.input module acemd.licensing module acemd.minimizer module acemd.nnp module acemd.protocols module acemd.reporters module acemd.restraints module acemd.system module acemd.utils module acemd.versionwarnings module acemd_register() (in module acemd.licensing) aliases (acemd.reporters.LoggingReporter attribute) aliases2 (acemd.reporters.LoggingReporter attribute) ANGLES (acemd.acemd.FGROUPS attribute) ANITorch (class in acemd.nnp) B BAROSTAT (acemd.acemd.FGROUPS attribute) BONDS (acemd.acemd.FGROUPS attribute) bracket_and_golden_section_search() (in module acemd.minimizer) C cgmin_compute() (in module acemd.minimizer) cleanup_charmm_prm() (in module acemd.charmm) CMAP (acemd.acemd.FGROUPS attribute) create_forcefield() (in module acemd.system) CustomReporter (class in acemd.reporters) D DEBUG (acemd.acemd.FGROUPS attribute) describeNextReport() (acemd.reporters.CustomReporter method) (acemd.reporters.LoggingReporter method) detect_input_file() (in module acemd.input) DIHEDRALS (acemd.acemd.FGROUPS attribute) E EXTERNAL (acemd.acemd.FGROUPS attribute) F FGROUPS (class in acemd.acemd) field_widths (acemd.reporters.LoggingReporter attribute) find_file() (in module acemd.acemd) forward() (acemd.nnp.ANITorch method) (acemd.nnp.TorchMDNETForce method) from_restraint_dict() (acemd.restraints.PositionalRestraint static method) from_restraint_str() (acemd.restraints.PositionalRestraint static method) G get_acemd_system() (in module acemd.acemd) get_cellular_restraints() (in module acemd.protocols) get_energy_decomposition() (in module acemd.acemd) get_energy_forces() (in module acemd.minimizer) get_force_str() (in module acemd.restraints) get_sim_properties() (in module acemd.acemd) I IMPLICIT (acemd.acemd.FGROUPS attribute) IMPROPER (acemd.acemd.FGROUPS attribute) L load_molecule() (in module acemd.acemd) LoggingReporter (class in acemd.reporters) M minimize() (in module acemd.minimizer) module acemd.acemd acemd.charmm acemd.input acemd.licensing acemd.minimizer acemd.nnp acemd.protocols acemd.reporters acemd.restraints acemd.system acemd.utils acemd.versionwarnings N NNP (acemd.acemd.FGROUPS attribute) NONBONDED (acemd.acemd.FGROUPS attribute) O openmm_to_molecule() (in module acemd.system) P parse_input_file() (in module acemd.input) parse_restraint() (acemd.restraints.PositionalRestraint static method) parse_setpoint() (in module acemd.restraints) parse_setpoints() (in module acemd.restraints) PLUMED (acemd.acemd.FGROUPS attribute) plumed_parser() (in module acemd.utils) PositionalRestraint (class in acemd.restraints) print_energy_decomposition() (in module acemd.acemd) R report() (acemd.reporters.CustomReporter method) (acemd.reporters.LoggingReporter method) run() (in module acemd.acemd) S setup_acemd() (in module acemd.acemd) setup_barostat() (in module acemd.acemd) setup_equilibration() (in module acemd.protocols) setup_extforces() (in module acemd.restraints) setup_nnp() (in module acemd.nnp) setup_production() (in module acemd.protocols) setup_pure_nnp_system() (in module acemd.nnp) setup_reporters() (in module acemd.reporters) setupForce() (acemd.restraints.PositionalRestraint method) SpeedLogger (class in acemd.reporters) step() (acemd.reporters.SpeedLogger method) T to_dict() (acemd.restraints.PositionalRestraint method) TorchMDNETForce (class in acemd.nnp) U update_restraints() (in module acemd.restraints) UREYBRADLEY (acemd.acemd.FGROUPS attribute) V view_forces() (in module acemd.utils)
