Index A | B | C | D | E | F | G | I | L | M | N | O | P | R | S | T | U | V A acemd module 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 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)
