diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py index e1efeb8..fc72590 100644 --- a/openfe_gromacs/protocols/gromacs_md/md_methods.py +++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py @@ -919,7 +919,9 @@ def _execute( output_dict["edr_em"] = shared_basepath / output_settings_em.edr_file output_dict["log_em"] = shared_basepath / output_settings_em.log_file output_dict["cpt_em"] = shared_basepath / output_settings_em.cpt_file - output_dict["grompp_mdp_em"] = shared_basepath / output_settings_em.grompp_mdp_file + output_dict["grompp_mdp_em"] = ( + shared_basepath / output_settings_em.grompp_mdp_file + ) # ToDo: Should we disallow running MD without EM? # Run NVT @@ -956,7 +958,9 @@ def _execute( output_dict["edr_nvt"] = shared_basepath / output_settings_nvt.edr_file output_dict["log_nvt"] = shared_basepath / output_settings_nvt.log_file output_dict["cpt_nvt"] = shared_basepath / output_settings_nvt.cpt_file - output_dict["grompp_mdp_nvt"] = shared_basepath / output_settings_nvt.grompp_mdp_file + output_dict["grompp_mdp_nvt"] = ( + shared_basepath / output_settings_nvt.grompp_mdp_file + ) # Run NPT MD simulation if sim_settings_npt.nsteps > 0: @@ -996,6 +1000,8 @@ def _execute( output_dict["edr_npt"] = shared_basepath / output_settings_npt.edr_file output_dict["log_npt"] = shared_basepath / output_settings_npt.log_file output_dict["cpt_npt"] = shared_basepath / output_settings_npt.cpt_file - output_dict["grompp_mdp_nvt"] = shared_basepath / output_settings_nvt.grompp_mdp_file + output_dict["grompp_mdp_nvt"] = ( + shared_basepath / output_settings_nvt.grompp_mdp_file + ) return output_dict diff --git a/openfe_gromacs/protocols/gromacs_md/md_settings.py b/openfe_gromacs/protocols/gromacs_md/md_settings.py index d22acdb..f6a5e0b 100644 --- a/openfe_gromacs/protocols/gromacs_md/md_settings.py +++ b/openfe_gromacs/protocols/gromacs_md/md_settings.py @@ -267,7 +267,7 @@ class OutputSettings(SettingsBaseModel): """ grompp_mdp_file: str = "mdout_em.mdp" """ - Filename for the mdp file that gmx grompp outputs. This file contains + Filename for the mdp file that gmx grompp outputs. This file contains comment lines, as well as the input that gmx grompp has read. Default 'mdout_em.mdp' """