From 3b52d29f73bb425b034898e6d8d2a7f5ddc36218 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 21 Mar 2024 13:56:35 +0000 Subject: [PATCH] Use Langevin integrator for free-energy simulations. --- python/BioSimSpace/_Config/_gromacs.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/python/BioSimSpace/_Config/_gromacs.py b/python/BioSimSpace/_Config/_gromacs.py index 23c50e613..010985613 100644 --- a/python/BioSimSpace/_Config/_gromacs.py +++ b/python/BioSimSpace/_Config/_gromacs.py @@ -207,10 +207,14 @@ def createConfig(self, version=None, extra_options={}, extra_lines=[]): # Temperature control. if not isinstance(self._protocol, _Protocol.Minimisation): - # Leap-frog molecular dynamics. - protocol_dict["integrator"] = "md" - # Temperature coupling using velocity rescaling with a stochastic term. - protocol_dict["tcoupl"] = "v-rescale" + if isinstance(self._protocol, _FreeEnergyMixin): + # Langevin dynamics. + protocol_dict["integrator"] = "sd" + else: + # Leap-frog molecular dynamics. + protocol_dict["integrator"] = "md" + # Temperature coupling using velocity rescaling with a stochastic term. + protocol_dict["tcoupl"] = "v-rescale" # A single temperature group for the entire system. protocol_dict["tc-grps"] = "system" # Thermostat coupling frequency (ps).