rid.common.gromacs package

Submodules

rid.common.gromacs.command module

rid.common.gromacs.command.get_grompp_cmd(mdp: Optional[str] = None, conf: Optional[str] = None, topology: Optional[str] = None, ref: Optional[str] = None, index: Optional[str] = None, max_warning: Optional[int] = None, output: Optional[str] = None, extra_parameters: Optional[Union[List, str]] = None)

rid.common.gromacs.command.get_mdrun_cmd(tpr: Optional[str], plumed: Optional[str] = None, cpi: Optional[str] = None, ntmpi: Optional[int] = None, nt: Optional[int] = None, extra_parameters: Optional[Union[List, str]] = None)

rid.common.gromacs.gmx_constant module

rid.common.gromacs.mdp module

rid.common.gromacs.mdp.check_basic_argument(md_parameters_dict: Dict)

rid.common.gromacs.mdp.make_md_mdp_from_config(md_parameters_dict)

rid.common.gromacs.mdp.make_md_mdp_string(gmx_config)

rid.common.gromacs.mdp.make_mdp_from_json(task: str, inputs: Optional[Dict] = None) → Dict

rid.common.gromacs.mdp.modify_define(define: Union[str, List]) → Dict

rid.common.gromacs.mdp.modify_output(freq: Union[str, int], output_mode: str = 'both') → Dict

rid.common.gromacs.trjconv module

rid.common.gromacs.trjconv.generate_coords(trr: str, top: str, out_coord: str = 'coord.xvg', output_group: str = 'System', index: Optional[str] = None)

rid.common.gromacs.trjconv.generate_forces(trr: str, top: str, out_force: str = 'force.xvg', output_group: str = 'System', index: Optional[str] = None)

rid.common.gromacs.trjconv.slice_trjconv(xtc: str, top: str, selected_time: float, output_group: int = 0, output: str = 'conf.gro')