""" test run for gromacs calculator """
import unittest
from ase.calculators.gromacs import 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("""HISE for testing
20
3HISE N 1 1.966 1.938 1.722
3HISE H1 2 2.053 1.892 1.711
3HISE H2 3 1.893 1.882 1.683
3HISE H3 4 1.969 2.026 1.675
3HISE CA 5 1.939 1.960 1.866
3HISE HA 6 1.934 1.869 1.907
3HISE CB 7 2.055 2.041 1.927
3HISE HB1 8 2.141 2.007 1.890
3HISE HB2 9 2.043 2.137 1.903
3HISE ND1 10 1.962 2.069 2.161
3HISE CG 11 2.065 2.032 2.077
3HISE CE1 12 2.000 2.050 2.287
3HISE HE1 13 1.944 2.069 2.368
3HISE NE2 14 2.123 2.004 2.287
3HISE HE2 15 2.177 1.981 2.369
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()
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()
species_dir = SPECIES_DIR,
run_command = RUN_COMMAND)
CALC_QM3.set(output = 'hirshfeld')
CALC_MM = Gromacs(
init_structure_file = infile_name,
structure_file = 'gromacs_qm.g96', \
force_field = 'oplsaa',
water_model = 'tip3p',
base_filename = 'gromacs_qm',
doing_qmmm = True, freeze_qm = False,
index_filename = 'index.ndx',
define = '-DFLEXIBLE',
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,
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
def calc(self, **kwargs):
from ase.calculators.gromacs import Gromacs
return Gromacs(command=self.executable, **kwargs)
outfile.write(' 3HISE C 18 1.806 2.032 1.888 \n')
outfile.write(' 3HISE OT1 19 1.736 2.000 1.987 \n')
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()
""" 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()
""" test run for gromacs calculator """
from ase.test import NotAvailable
from ase.calculators.gromacs import Gromacs
if Gromacs().get_command() is None:
raise NotAvailable('Gromacs required')
import sys, os, glob
from ase.io import read, write
GRO_INIT_FILE = 'hise_box.gro'
#write structure file
outfile=open('hise_box.gro','w')
outfile.write('HISE for testing \n')
outfile.write(' 20 \n')
outfile.write(' 3HISE N 1 1.966 1.938 1.722 \n')
outfile.write(' 3HISE H1 2 2.053 1.892 1.711 \n')
outfile.write(' 3HISE H2 3 1.893 1.882 1.683 \n')
outfile.write(' 3HISE H3 4 1.969 2.026 1.675 \n')
outfile.write(' 3HISE CA 5 1.939 1.960 1.866 \n')
outfile.write(' 3HISE HA 6 1.934 1.869 1.907 \n')
outfile.write(' 3HISE CB 7 2.055 2.041 1.927 \n')
outfile.write(' 3HISE HB1 8 2.141 2.007 1.890 \n')
outfile.write(' 3HISE HB2 9 2.043 2.137 1.903 \n')
outfile.write(' 3HISE ND1 10 1.962 2.069 2.161 \n')
outfile.write(' 3HISE CG 11 2.065 2.032 2.077 \n')
outfile.write(' 3HISE CE1 12 2.000 2.050 2.287 \n')
outfile.write(' 3HISE HE1 13 1.944 2.069 2.368 \n')
