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[pre-commit.ci] auto fixes from pre-commit.com hooks
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pre-commit-ci[bot] committed Jul 16, 2024
1 parent 89486dc commit cbedd1a
Showing 1 changed file with 11 additions and 8 deletions.
19 changes: 11 additions & 8 deletions openfe_gromacs/protocols/gromacs_md/md_settings.py
Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand All @@ -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):
Expand All @@ -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
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