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
outfile.write(' 3HISE OT2 20 1.770 2.057 2.016 \n')
outfile.write(' 4.00000 4.00000 4.00000 \n')
outfile.close()
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', 'hise_box.gro')
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)
assert abs(final_energy + 4.06503308131) < 5e-3
outfile.close()
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', 'hise_box.gro')
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)
assert abs(final_energy + 4.06503308131) < 5e-3
""" An example for using gromacs calculator in ase.
Atom positions are relaxed.
A sample call:
python ./gromacs_example_mm_relax.py his.pdb
"""
from ase.calculators.gromacs import Gromacs
import sys
from ase.io import read
infile_name = sys.argv[1]
CALC_MM_RELAX = Gromacs(clean=True)
CALC_MM_RELAX.set_own_params_runs(
'extra_pdb2gmx_parameters','-ignh')
CALC_MM_RELAX.set_own_params_runs(
'init_structure',infile_name)
CALC_MM_RELAX.generate_topology_and_g96file()
CALC_MM_RELAX.write_input()
CALC_MM_RELAX.set_own_params_runs(
'extra_editconf_parameters','-bt cubic -c -d 0.8')
CALC_MM_RELAX.run_editconf()
CALC_MM_RELAX.set_own_params_runs(
'extra_genbox_parameters','-cs spc216.gro')
CALC_MM_RELAX.run_genbox()
CALC_MM_RELAX.generate_gromacs_run_file()
CALC_MM_RELAX.run()
""" An example for using gromacs calculator in ase.
Atom positions are relaxed.
A sample call:
python ./gromacs_example_mm_relax.py his.pdb
"""
from ase.calculators.gromacs import Gromacs
import sys
from ase.io import read
infile_name = sys.argv[1]
CALC_MM_RELAX = Gromacs(clean=True)
CALC_MM_RELAX.set_own_params_runs('extra_pdb2gmx_parameters', '-ignh')
CALC_MM_RELAX.set_own_params_runs('init_structure', infile_name)
CALC_MM_RELAX.generate_topology_and_g96file()
CALC_MM_RELAX.write_input()
CALC_MM_RELAX.set_own_params_runs('extra_editconf_parameters',
'-bt cubic -c -d 0.8')
CALC_MM_RELAX.run_editconf()
CALC_MM_RELAX.set_own_params_runs('extra_genbox_parameters', '-cs spc216.gro')
CALC_MM_RELAX.run_genbox()
CALC_MM_RELAX.generate_gromacs_run_file()
CALC_MM_RELAX.run()
