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"""An example for using gromacs calculator in ase.
Atom positions are relaxed.
A sample call:
python ./gromacs_example_mm_relax.py his.pdb
"""
import sys
from ase.calculators.gromacs import Gromacs
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()
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