Index _ | A | C | D | E | F | G | I | K | L | M | N | O | P | R | S | T | U | W _ __call__() (asyncmd.trajectory.functionwrapper.TrajectoryFunctionWrapper method) (asyncmd.trajectory.PyTrajectoryFunctionWrapper method) (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper method) __hash__() (asyncmd.Trajectory method) __len__() (asyncmd.Trajectory method) _get_id_str() (asyncmd.trajectory.functionwrapper.TrajectoryFunctionWrapper method) _get_values_for_trajectory() (asyncmd.trajectory.functionwrapper.TrajectoryFunctionWrapper method) _parse_line() (asyncmd.mdconfig.LineBasedMDConfig method) A apply_constraints() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) (asyncmd.mdengine.MDEngine method) apply_modification() (asyncmd.trajectory.convert.FrameExtractor method) (asyncmd.trajectory.InvertedVelocitiesFrameExtractor method) (asyncmd.trajectory.NoModificationFrameExtractor method) (asyncmd.trajectory.RandomVelocitiesFrameExtractor method) asyncmd module asyncmd.config module asyncmd.gromacs module asyncmd.gromacs.mdconfig module asyncmd.gromacs.mdengine module asyncmd.gromacs.utils module asyncmd.mdconfig module asyncmd.mdengine module asyncmd.slurm module asyncmd.tools module asyncmd.trajectory module asyncmd.trajectory.convert module asyncmd.trajectory.functionwrapper module asyncmd.trajectory.propagate module asyncmd.trajectory.trajectory module asyncmd.trajectory.trajectory_cache module asyncmd.utils module C call_kwargs (asyncmd.trajectory.functionwrapper.TrajectoryFunctionWrapper property) (asyncmd.trajectory.PyTrajectoryFunctionWrapper property) (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property) changed (asyncmd.gromacs.MDP property) (asyncmd.mdconfig.LineBasedMDConfig property) clear_all_cache_values() (asyncmd.Trajectory method) communicate() (asyncmd.slurm.SlurmProcess method) concatenate() (asyncmd.trajectory.TrajectoryConcatenator method) concatenate_async() (asyncmd.trajectory.TrajectoryConcatenator method) ConditionalTrajectoryPropagator (class in asyncmd.trajectory) conditions (asyncmd.trajectory.ConditionalTrajectoryPropagator property) construct_tp_from_plus_and_minus_traj_segments() (in module asyncmd.trajectory) current_trajectory (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) (asyncmd.mdengine.MDEngine property) cut_and_concatenate() (asyncmd.trajectory.ConditionalTrajectoryPropagator method) (asyncmd.trajectory.InPartsTrajectoryPropagator method) D deffnm (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) del_sbatch_option() (asyncmd.slurm.SlurmProcess method) dt (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) (asyncmd.Trajectory property) E EngineCrashedError EngineError exclude_nodes (asyncmd.slurm.SlurmClusterMediator property) executable (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property) extract() (asyncmd.trajectory.convert.FrameExtractor method) extract_async() (asyncmd.trajectory.convert.FrameExtractor method) F first_step (asyncmd.Trajectory property) first_time (asyncmd.Trajectory property) FrameExtractor (class in asyncmd.trajectory.convert) frames_done (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) function (asyncmd.trajectory.PyTrajectoryFunctionWrapper property) G generate_velocities() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) get_info_for_job() (asyncmd.slurm.SlurmClusterMediator method) GmxEngine (class in asyncmd.gromacs) gro_file (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) grompp_executable (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute) grompp_extra_args (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute) I id (asyncmd.trajectory.functionwrapper.TrajectoryFunctionWrapper property) (asyncmd.trajectory.PyTrajectoryFunctionWrapper property) (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property) InPartsTrajectoryPropagator (class in asyncmd.trajectory) invert_v_for_negative_step (asyncmd.trajectory.TrajectoryConcatenator attribute) InvertedVelocitiesFrameExtractor (class in asyncmd.trajectory) K kill() (asyncmd.slurm.SlurmProcess method) L last_step (asyncmd.Trajectory property) last_time (asyncmd.Trajectory property) LineBasedMDConfig (class in asyncmd.mdconfig) list_all_nodes() (asyncmd.slurm.SlurmClusterMediator method) M mdconfig (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) MDConfig (class in asyncmd.mdconfig) MDEngine (class in asyncmd.mdengine) mdp (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) MDP (class in asyncmd.gromacs) mdrun_executable (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute) mdrun_extra_args (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute) mdrun_time_conversion_factor (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute) min_time_between_sacct_calls (asyncmd.slurm.SlurmClusterMediator attribute) module asyncmd asyncmd.config asyncmd.gromacs asyncmd.gromacs.mdconfig asyncmd.gromacs.mdengine asyncmd.gromacs.utils asyncmd.mdconfig asyncmd.mdengine asyncmd.slurm asyncmd.tools asyncmd.trajectory asyncmd.trajectory.convert asyncmd.trajectory.functionwrapper asyncmd.trajectory.propagate asyncmd.trajectory.trajectory asyncmd.trajectory.trajectory_cache asyncmd.utils monitor_register_job() (asyncmd.slurm.SlurmClusterMediator method) monitor_remove_job() (asyncmd.slurm.SlurmClusterMediator method) N ndx_file (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) nodes (asyncmd.slurm.SlurmProcess property) NoModificationFrameExtractor (class in asyncmd.trajectory) nstout (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) (asyncmd.Trajectory property) num_fails_for_broken_node (asyncmd.slurm.SlurmClusterMediator attribute) O original_file (asyncmd.gromacs.MDP property) (asyncmd.mdconfig.LineBasedMDConfig property) output_traj_type (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute) (asyncmd.mdengine.MDEngine property) P parse() (asyncmd.gromacs.MDP method) (asyncmd.mdconfig.LineBasedMDConfig method) (asyncmd.mdconfig.MDConfig method) prepare() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) (asyncmd.mdengine.MDEngine method) prepare_from_files() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) (asyncmd.mdengine.MDEngine method) propagate() (asyncmd.trajectory.ConditionalTrajectoryPropagator method) (asyncmd.trajectory.InPartsTrajectoryPropagator method) propagate_and_concatenate() (asyncmd.trajectory.ConditionalTrajectoryPropagator method) (asyncmd.trajectory.InPartsTrajectoryPropagator method) PyTrajectoryFunctionWrapper (class in asyncmd.trajectory) R RandomVelocitiesFrameExtractor (class in asyncmd.trajectory) register_h5py_cache() (in module asyncmd.config) remove_double_frames (asyncmd.trajectory.TrajectoryConcatenator attribute) remove_parts() (asyncmd.trajectory.ConditionalTrajectoryPropagator method) (asyncmd.trajectory.InPartsTrajectoryPropagator method) returncode (asyncmd.slurm.SlurmProcess property) run() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) run_steps() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) (asyncmd.mdengine.MDEngine method) run_walltime() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) (asyncmd.mdengine.MDEngine method) S sacct_executable (asyncmd.slurm.SlurmClusterMediator attribute) sbatch_executable (asyncmd.slurm.SlurmProcess attribute) sbatch_options (asyncmd.slurm.SlurmProcess property) (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property) sbatch_script (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property) scancel_executable (asyncmd.slurm.SlurmProcess attribute) set_max_files_open() (in module asyncmd.config) set_max_process() (in module asyncmd.config) set_sbatch_option() (asyncmd.slurm.SlurmProcess method) set_slurm_max_jobs() (in module asyncmd.config) set_slurm_settings() (in module asyncmd.config) set_trajectory_cache_type() (in module asyncmd.config) show_config() (in module asyncmd.config) simulation_part (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) sinfo_executable (asyncmd.slurm.SlurmClusterMediator attribute) sleep_time (asyncmd.slurm.SlurmProcess attribute) slurm_cluster_mediator (asyncmd.slurm.SlurmProcess property) slurm_job_state (asyncmd.slurm.SlurmProcess property) slurm_jobid (asyncmd.slurm.SlurmProcess property) slurm_jobname (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property) SlurmClusterMediator (class in asyncmd.slurm) SlurmGmxEngine (class in asyncmd.gromacs) SlurmProcess (class in asyncmd.slurm) SlurmTrajectoryFunctionWrapper (class in asyncmd.trajectory) stdfiles_removal (asyncmd.slurm.SlurmProcess property) steps_done (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) (asyncmd.mdengine.MDEngine property) structure_file (asyncmd.Trajectory property) submit() (asyncmd.slurm.SlurmProcess method) success_to_fail_ratio (asyncmd.slurm.SlurmClusterMediator attribute) T T (asyncmd.trajectory.RandomVelocitiesFrameExtractor attribute) terminate() (asyncmd.slurm.SlurmProcess method) time (asyncmd.slurm.SlurmProcess property) time_done (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) top_file (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) tpr_file (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) Trajectory (class in asyncmd) trajectory_files (asyncmd.Trajectory property) trajectory_hash (asyncmd.Trajectory property) TrajectoryConcatenator (class in asyncmd.trajectory) TrajectoryFunctionWrapper (class in asyncmd.trajectory.functionwrapper) U update_cache_type() (asyncmd.Trajectory method) W wait() (asyncmd.slurm.SlurmProcess method) workdir (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) write() (asyncmd.gromacs.MDP method) (asyncmd.mdconfig.LineBasedMDConfig method) (asyncmd.mdconfig.MDConfig method)
