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Allow use of gmx_mpi #406

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Allow use of gmx_mpi #406

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6e0390d
ENH: use gmx_mpi if available
jotelha Jan 28, 2026
c34b94c
MAINT: don't set the number of threads for gmx ecplicitly, as setting…
jotelha Jan 28, 2026
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8 changes: 7 additions & 1 deletion intermol/gromacs/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,12 @@ def gmx_path(binary_path):
grompp_bin = [gmx_path('grompp')]
mdrun_bin = [gmx_path('mdrun')]
genergy_bin = [gmx_path('g_energy')]
elif which('gmx_mpi'):
logger.debug("Using MPI-parallel binaries")
main_binary = gmx_path('gmx_mpi')
grompp_bin = [main_binary, 'grompp']
mdrun_bin = [main_binary, 'mdrun']
genergy_bin = [main_binary, 'energy']
else:
raise IOError('Unable to find gromacs executables.')
return grompp_bin, mdrun_bin, genergy_bin
Expand Down Expand Up @@ -112,7 +118,7 @@ def energies(top, gro, mdp, gmx_path=GMX_PATH, grosuff='', grompp_check=False):
logger.error(f'grompp failed with error code {proc.returncode} See {stderr_path}')

# Run single-point calculation with mdrun.
mdrun_bin.extend(['-nt', '1', '-s', tpr, '-o', traj, '-cpo', state, '-c', conf, '-e', ener, '-g', log])
mdrun_bin.extend(['-s', tpr, '-o', traj, '-cpo', state, '-c', conf, '-e', ener, '-g', log])
proc = run_subprocess(mdrun_bin, 'gromacs', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('mdrun failed. See %s' % stderr_path)
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