Index C | D | E | F | G | I | M | N | O | P | R | S | T | U C create() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocol method) D data (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult property) default_settings() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocol class method) dependencies (openfe_gromacs.protocols.gromacs_md.GromacsMDRunUnit property) (openfe_gromacs.protocols.gromacs_md.GromacsMDSetupUnit property) E engine_settings (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) execute() (openfe_gromacs.protocols.gromacs_md.GromacsMDRunUnit method) (openfe_gromacs.protocols.gromacs_md.GromacsMDSetupUnit method) F forcefield_settings (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) frozen_copy() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings method) G gather() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocol method) get_defaults() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings class method) get_estimate() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_filenames_em() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_filenames_npt() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_filenames_nvt() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_gro_em_filenames() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_gro_filename() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_gro_npt_filenames() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_gro_nvt_filenames() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_mdp_filenames() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_top_filename() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_uncertainty() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_xtc_em_filenames() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_xtc_npt_filenames() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) get_xtc_nvt_filenames() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult method) gro (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) GromacsMDProtocol (class in openfe_gromacs.protocols.gromacs_md) GromacsMDProtocolResult (class in openfe_gromacs.protocols.gromacs_md) GromacsMDRunUnit (class in openfe_gromacs.protocols.gromacs_md) GromacsMDSetupUnit (class in openfe_gromacs.protocols.gromacs_md) I inputs (openfe_gromacs.protocols.gromacs_md.GromacsMDRunUnit property) (openfe_gromacs.protocols.gromacs_md.GromacsMDSetupUnit property) integrator_settings (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) is_frozen (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings property) M module openfe_gromacs.protocols.gromacs_md openfe_gromacs.protocols.gromacs_md.md_settings must_be_positive() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings class method) N n_protocol_dag_results (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult property) name (openfe_gromacs.protocols.gromacs_md.GromacsMDRunUnit property) (openfe_gromacs.protocols.gromacs_md.GromacsMDSetupUnit property) O openfe_gromacs.protocols.gromacs_md module openfe_gromacs.protocols.gromacs_md.md_settings module output_settings_em (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) output_settings_npt (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) output_settings_nvt (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) P partial_charge_settings (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) protocol_repeats (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) R result_cls (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocol attribute) run() (openfe_gromacs.protocols.gromacs_md.GromacsMDSetupUnit method) S settings (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocol property) simulation_settings_em (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) simulation_settings_npt (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) simulation_settings_nvt (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) solvation_settings (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) T thermo_settings (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) top (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings attribute) (openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings attribute) U unfrozen_copy() (openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolSettings method)