From cbedd1a591ef5d01a1cc7e8fb4f700a363b57fee Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 16 Jul 2024 11:22:38 +0000 Subject: [PATCH] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .../protocols/gromacs_md/md_settings.py | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/openfe_gromacs/protocols/gromacs_md/md_settings.py b/openfe_gromacs/protocols/gromacs_md/md_settings.py index 1d702e3..4b37c2e 100644 --- a/openfe_gromacs/protocols/gromacs_md/md_settings.py +++ b/openfe_gromacs/protocols/gromacs_md/md_settings.py @@ -687,9 +687,9 @@ class EMSimulationSettings(SimulationSettings): """ Initial step size. Default 0.01 * unit.nanometer """ - tcoupl = 'no' - pcoupl = 'no' - gen_vel = 'no' + tcoupl = "no" + pcoupl = "no" + gen_vel = "no" class EMOutputSettings(OutputSettings): @@ -702,9 +702,10 @@ class NVTSimulationSettings(SimulationSettings): """ Settings for MD simulation in the NVT ensemble. """ + nsteps = 50000 # 100ps - pcoupl = 'no' - gen_vel = 'yes' + pcoupl = "no" + gen_vel = "yes" class NVTOutputSettings(OutputSettings): @@ -717,16 +718,18 @@ class NPTSimulationSettings(SimulationSettings): """ Settings for MD simulation in the NPT ensemble. """ - pcoupl = 'Parrinello-Rahman' - pcoupltype = 'isotropic' + + pcoupl = "Parrinello-Rahman" + pcoupltype = "isotropic" ref_p = 1.01325 * unit.bar - gen_vel = 'no' # If continuation from NVT simulation + gen_vel = "no" # If continuation from NVT simulation class NPTOutputSettings(OutputSettings): """ Output Settings for the MD simulation in the NPT ensemble. """ + nstxout = 5000 nstvout = 5000 nstfout = 5000