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Fix issue #484 #485

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Merged
lohedges merged 2 commits into from
Dec 3, 2025
Merged

Fix issue #484 #485

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f4e9cd4
Update GROMACS NPT config to match sandpit. [closes #484]
lohedges Dec 3, 2025
e3add88
Correctly scale tau-p according to dt and nstpcouple.
lohedges Dec 3, 2025
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5 changes: 2 additions & 3 deletions python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -535,9 +535,8 @@ def generateGromacsConfig(
protocol_dict["pcoupl"] = "Berendsen" # Berendsen barostat.
# Do the MC move every 100 steps to be the same as AMBER.
protocol_dict["nstpcouple"] = 100
# 4ps time constant for pressure coupling.
# As the tau-p has to be 10 times larger than nstpcouple * dt (4 fs)
protocol_dict["tau-p"] = 4
# 25 times larger than nstpcouple * dt.
protocol_dict["tau-p"] = 2500 * timestep
protocol_dict["ref-p"] = (
f"{self.protocol.getPressure().bar().value():.5f}" # Pressure in bar.
)
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6 changes: 4 additions & 2 deletions python/BioSimSpace/_Config/_gromacs.py
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Expand Up @@ -186,8 +186,10 @@ def createConfig(self, version=None, extra_options={}, extra_lines=[]):
protocol_dict["pcoupl"] = "c-rescale"
else:
protocol_dict["pcoupl"] = "berendsen"
# 1ps time constant for pressure coupling.
protocol_dict["tau-p"] = 1
# Do the MC move every 100 steps to be the same as AMBER.
protocol_dict["nstpcouple"] = 100
# 25 times larger than nstpcouple * dt.
protocol_dict["tau-p"] = 2500 * timestep
# Pressure in bar.
protocol_dict["ref-p"] = (
f"{self._protocol.getPressure().bar().value():.5f}"
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