def test_gromacs():
g = Gromacs()
if g.command is None:
raise unittest.SkipTest(getattr(g, "missing_gmx", "missing gromacs"))
GRO_INIT_FILE = 'hise_box.gro'
# write structure file
with open(GRO_INIT_FILE, 'w') as outfile:
outfile.write(data)
CALC_MM_RELAX = Gromacs(force_field='charmm27',
define='-DFLEXIBLE',
integrator='cg',
nsteps='10000',
nstfout='10',
nstlog='10',
nstenergy='10',
nstlist='10',
ns_type='grid',
pbc='xyz',
rlist='0.7',
coulombtype='PME-Switch',
rcoulomb='0.6',
vdwtype='shift',
rvdw='0.6',
rvdw_switch='0.55',
DispCorr='Ener')
CALC_MM_RELAX.set_own_params_runs('init_structure', GRO_INIT_FILE)
CALC_MM_RELAX.generate_topology_and_g96file()
CALC_MM_RELAX.write_input()
CALC_MM_RELAX.generate_gromacs_run_file()
CALC_MM_RELAX.run()
atoms = CALC_MM_RELAX.get_atoms()
final_energy = CALC_MM_RELAX.get_potential_energy(atoms)
# e.g., -4.17570101 eV = -402.893902 kJ / mol by Gromacs 2019.1 double precision
final_energy_ref = -4.175
tolerance = 0.010
assert abs(final_energy - final_energy_ref) < tolerance
CALC_MM_RELAX = Gromacs(force_field='charmm27',
define='-DFLEXIBLE',
integrator='cg',
nsteps='10000',
nstfout='10',
nstlog='10',
nstenergy='10',
nstlist='10',
ns_type='grid',
pbc='xyz',
rlist='0.7',
coulombtype='PME-Switch',
rcoulomb='0.6',
vdwtype='shift',
rvdw='0.6',
rvdw_switch='0.55',
DispCorr='Ener')
CALC_MM_RELAX.set_own_params_runs('init_structure', GRO_INIT_FILE)
CALC_MM_RELAX.generate_topology_and_g96file()
CALC_MM_RELAX.write_input()
CALC_MM_RELAX.generate_gromacs_run_file()
CALC_MM_RELAX.run()
atoms = CALC_MM_RELAX.get_atoms()
final_energy = CALC_MM_RELAX.get_potential_energy(atoms)
# e.g., -4.17570101 eV = -402.893902 kJ / mol by Gromacs 2019.1 double precision
final_energy_ref = -4.175
tolerance = 0.010
assert abs(final_energy - final_energy_ref) < tolerance
infile_name = sys.argv[1]
CALC_MM_RELAX = Gromacs(
init_structure_file=infile_name,
structure_file = 'gromacs_mm-relax.g96',
force_field='oplsaa',
water_model='tip3p',
base_filename = 'gromacs_mm-relax',
doing_qmmm = False, freeze_qm = True,
index_filename = 'index.ndx',
extra_mdrun_parameters = ' -nt 1 ',
define = '-DFLEXIBLE',
integrator = 'cg',
nsteps = '10000',
nstfout = '10',
nstlog = '10',
nstenergy = '10',
nstlist = '10',
ns_type = 'grid',
pbc = 'xyz',
rlist = '1.15',
coulombtype = 'PME-Switch',
rcoulomb = '0.8',
vdwtype = 'shift',
rvdw = '0.8',
rvdw_switch = '0.75',
DispCorr = 'Ener')
CALC_MM_RELAX.generate_topology_and_g96file()
CALC_MM_RELAX.generate_gromacs_run_file()
CALC_MM_RELAX.run()
integrator = 'md',
nsteps = '0',
nstfout = '1',
nstlog = '1',
nstenergy = '1',
nstlist = '1',
ns_type = 'grid',
pbc = 'xyz',
rlist = '1.15',
coulombtype = 'PME-Switch',
rcoulomb = '0.8',
vdwtype = 'shift',
rvdw = '0.8',
rvdw_switch = '0.75',
DispCorr = 'Ener')
CALC_MM.generate_topology_and_g96file()
CALC_MM.generate_gromacs_run_file()
CALC_QMMM = AseQmmmManyqm(nqm_regions = 3,
qm_calculators = [CALC_QM1, CALC_QM2, CALC_QM3],
mm_calculator = CALC_MM,
link_info = 'byQM')
# link_info = 'byFILE')
SYSTEM = read_gromos('gromacs_qm.g96')
SYSTEM.set_calculator(CALC_QMMM)
DYN = BFGS(SYSTEM)
DYN.run(fmax = 0.05)
print('exiting fine')
LOG_FILE.close()
integrator = 'md',
nsteps = '0',
nstfout = '1',
nstlog = '1',
nstenergy = '1',
nstlist = '1',
ns_type = 'grid',
pbc = 'xyz',
rlist = '1.15',
coulombtype = 'PME-Switch',
rcoulomb = '0.8',
vdwtype = 'shift',
rvdw = '0.8',
rvdw_switch = '0.75',
DispCorr = 'Ener')
CALC_MM.generate_topology_and_g96file()
CALC_MM.generate_gromacs_run_file()
CALC_QMMM = AseQmmmManyqm(nqm_regions=3,
qm_calculators=[CALC_QM1, CALC_QM2, CALC_QM3],
mm_calculator=CALC_MM,
link_info='byQM')
# link_info = 'byFILE')
SYSTEM = read('gromacs_qm.g96')
SYSTEM.calc = CALC_QMMM
DYN = BFGS(SYSTEM)
DYN.run(fmax=0.05)
print('exiting fine')
LOG_FILE.close()
