def test_gmx_tip4p():
mol = Topology.open(cwd + '/../topology/files/TIP3P.zmat').molecules[0]
ff = ForceField.open(cwd + '/../forcefield/files/TIP4P.zfp')
mol.generate_virtual_sites(ff)
mol.assign_charge_from_ff(ff)
top = Topology([mol], numbers=[100], cell=UnitCell([3, 3, 3]))
top.set_positions(Topology.open(cwd + '/files/100-TIP4P.pdb').positions)
system = System(top, ff)
tmpgro = os.path.join(tmpdir, 'conf-vsite.gro')
tmptop = os.path.join(tmpdir, 'topol-vsite.top')
tmpmdp = os.path.join(tmpdir, 'grompp-vsite.mdp')
system.export_gromacs(gro_out=tmpgro, top_out=tmptop, mdp_out=tmpmdp)
assert filecmp.cmp(tmpgro, cwd + '/files/baselines/conf-vsite.gro')
assert filecmp.cmp(tmptop, cwd + '/files/baselines/topol-vsite.top')
assert filecmp.cmp(tmpmdp, cwd + '/files/baselines/grompp-vsite.mdp')
def test_tip4p():
mol = Topology.open(cwd + '/../topology/files/TIP3P.zmat').molecules[0]
ff = ForceField.open(cwd + '/../forcefield/files/TIP4P.zfp')
mol.generate_virtual_sites(ff)
mol.assign_charge_from_ff(ff)
top = Topology([mol], numbers=[100], cell=UnitCell([3, 3, 3]))
top.set_positions(Topology.open(cwd + '/files/100-TIP4P.pdb').positions)
system = System(top, ff)
context = mm.Context(system.to_omm_system(), *get_omm_integrator_platform())
context.setPositions(top.positions)
print_energy_terms(context)
pe = context.getState(getEnergy=True).getPotentialEnergy().value_in_unit(kJ_mol)
assert pytest.approx(pe, rel=0.001) == 383.796 # results of GROMACS
if args.packmol:
top.update_molecules(list(mol_count.keys()))
top.scale_with_packmol(list(mol_count.values()))
sys.exit(0)
logger.info('Exporting ...')
top.update_molecules(list(mol_count.keys()), list(mol_count.values()))
if args.trj is None:
logger.warning('Trajectory file not provided. '
'Will use positions and cell from the topology')
else:
_positions_set = False
if len(frame.positions) == top.n_atom:
top.set_positions(frame.positions)
_positions_set = True
elif ff.is_polarizable or ff.has_virtual_site:
atoms_real = [atom for atom in top.atoms if not atom.is_drude and atom.virtual_site is None]
if len(frame.positions) == len(atoms_real):
for i, atom in enumerate(atoms_real):
atom.position = frame.positions[i][:]
np.random.seed(1)
for parent, drude in top.get_drude_pairs():
drude.position = parent.position + (np.random.random(3) - 0.5) / 100
for parent, vsite in top.get_virtual_site_pairs():
vsite.position = vsite.virtual_site.calc_position()
_positions_set = True
if not _positions_set:
logger.error(
