def _run_fep(self, solvent, dirname):
cfg = get_configuration('runinput.yml')
if gromacs.release.startswith('4'):
# For GROMACS 4.6.5 explicitly enable the group neighbor
# scheme by creating a copy of the MDP file in the current
# directory with MDP cutoff-scheme option changed. The local
# MDP file will be picked up in preference to the default one
# in the templates.
fep_mdp_name = cfg.get("FEP", "mdp")
mdp = mdpow.config.get_template(fep_mdp_name)
gromacs.cbook.edit_mdp(mdp,
new_mdp=os.path.join(
os.getcwd(), fep_mdp_name),
cutoff_scheme="group")
self.S = fep_simulation(cfg, solvent, dirname=dirname)
def _run_equil(self, solvent, dirname):
cfg = get_configuration('runinput.yml')
self.S = equilibrium_simulation(cfg, solvent, dirname=dirname)
def _run_fep(self, solvent, dirname):
cfg = get_configuration('runinput.yml')
self.S = fep_simulation(cfg, solvent, dirname=dirname)
def cfg(self):
return config.get_configuration(
str(CONFIGURATIONS / 'altered_runinput.yml'))