def __init__(self, gromacs_dir, label='opls-aa', pair_cutoff=10.0, kspace=False, **kwargs):
LAMMPSBase.__init__(self, label, **kwargs)
self.parameters.units = 'real'
if kspace:
self.parameters.pair_style = 'lj/cut/coul/long %f' % pair_cutoff
self.parameters.kspace_style = 'ewald 0.0001'
else:
self.parameters.pair_style = 'lj/cut/coul/cut %f' % pair_cutoff
self.parameters.pair_modify = 'mix geometric'
self.parameters.bond_style = 'harmonic'
self.parameters.angle_style = 'harmonic'
self.parameters.dihedral_style = 'multi/harmonic'
#self.parameters.improper_style = 'harmonic'
self.parameters.special_bonds = 'lj/coul 0.0 0.0 0.5'
# Read force field file
ffnonbonded = os.path.join(gromacs_dir, 'oplsaa.ff', 'ffnonbonded.itp')
ffbonded = os.path.join(gromacs_dir, 'oplsaa.ff', 'ffbonded.itp')
self.ff_data, self.charges = read_gromacs_params.read((ffnonbonded, ffbonded), return_charges=True)
self.type_resolver = typing.TypeResolver(oplsaatypes.data)
# Add parameters for flexible TIP3P water
self.ff_data.add('bond', SequenceType(['OW', 'HW']), 'Bond Coeffs', [450, 0.9572])
self.ff_data.add('angle', SequenceType(['HW', 'OW', 'HW']), 'Angle Coeffs', [55, 104.52])
def __init__(self, gromacs_dir, label='amber', inner_cutoff = 8.0, outer_cutoff=10.0, **kwargs): LAMMPSBase.__init__(self, label, **kwargs) self.parameters.units = 'real' self.parameters.pair_style = 'lj/charmm/coul/charmm %f %f' % (inner_cutoff, outer_cutoff) self.parameters.bond_style = 'harmonic' self.parameters.angle_style = 'harmonic' self.parameters.dihedral_style = 'charmm' #self.parameters.improper_style = 'harmonic' self.parameters.special_bonds = 'amber' # Read force field file ffnonbonded = os.path.join(gromacs_dir, 'amber03.ff', 'ffnonbonded.itp') ffbonded = os.path.join(gromacs_dir, 'amber03.ff', 'ffbonded.itp') self.ff_data = read_gromacs_params.read((ffnonbonded, ffbonded)) self.type_resolver = typing.TypeResolver(ambertypes.data)