def energy(prm, crd, mdin):
"""Evaluate the energy of a .prmtop, .inpcrd and .in file combination.
Parameters
----------
prm : str
crd : str
mdin : str
Returns
-------
energies : OrderedDict
"""
mdin = os.path.abspath(mdin)
directory, _ = os.path.split(os.path.abspath(prm))
mdout = ''
stdout_path = os.path.join(directory, 'amber_stdout.txt')
stderr_path = os.path.join(directory, 'amber_stderr.txt')
# Run sander.
sander = ['sander']
sander.extend(['-i', mdin,
'-O', mdout,
'-p', prm,
'-c', crd,
'-O', mdout])
run_subprocess(sander, stdout_path, stderr_path)
# TODO: Fix mdout filenaming.
energy = _parse_energy_mdout(mdout or 'mdout')
return canonicalize_energy_names(energy, 'amber')
def energy(top, gro, mdp):
"""Evaluate the energy of a .top, .gro and .mdp file combination.
Parameters
----------
top : str
gro : str
mdp : str
Returns
-------
energies : OrderedDict
"""
mdp = os.path.abspath(mdp)
directory, _ = os.path.split(os.path.abspath(top))
tpr = os.path.join(directory, 'topol.tpr')
ener = os.path.join(directory, 'ener.edr')
ener_xvg = os.path.join(directory, 'energy.xvg')
conf = os.path.join(directory, 'confout.gro')
mdout = os.path.join(directory, 'mdout.mdp')
state = os.path.join(directory, 'state.cpt')
traj = os.path.join(directory, 'traj.trr')
log = os.path.join(directory, 'md.log')
stdout_path = os.path.join(directory, 'gromacs_stdout.txt')
stderr_path = os.path.join(directory, 'gromacs_stderr.txt')
grompp, mdrun, genergy = binaries()
# Run grompp.
grompp.extend(['-f', mdp,
'-c', gro,
'-p', top,
'-o', tpr,
'-po', mdout,
'-maxwarn', '5'])
run_subprocess(grompp, stdout_path, stderr_path)
# Run single-point calculation with mdrun.
mdrun.extend(['-nt', '1',
'-s', tpr,
'-o', traj,
'-cpo', state,
'-c', conf,
'-e', ener,
'-g', log])
run_subprocess(mdrun, stdout_path, stderr_path)
# Extract energies using g_energy
select = " ".join(map(str, range(1, 20))) + " 0 "
genergy.extend(['-f', ener,
'-o', ener_xvg,
'-dp'])
run_subprocess(genergy, stdout_path, stderr_path, stdin=select)
energy = _parse_energy_xvg(ener_xvg)
return canonicalize_energy_names(energy, 'gromacs')