def __init__(self,
ff_file_path,
label='compass',
pair_cutoff=9.5,
kspace=False,
**kwargs):
LAMMPSBase.__init__(self, label, **kwargs)
self.parameters.units = 'real'
if kspace:
self.parameters.pair_style = 'lj/class2/coul/long %f' % pair_cutoff
self.parameters.kspace_style = 'ewald 0.0001'
else:
self.parameters.pair_style = 'lj/class2/coul/cut %f' % pair_cutoff
self.parameters.bond_style = 'class2'
self.parameters.angle_style = 'class2'
self.parameters.dihedral_style = 'class2'
self.parameters.improper_style = 'class2'
self.parameters.special_bonds = 'lj/coul 0.0 0.0 1.0 dihedral yes'
self.ff_data, self.bond_increments = read_compass_params.read(
open(ff_file_path))
self.type_resolver = typing.TypeResolver(compasstypes.data)
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)
def __init__(self, label='clayff', pair_cutoff=(10.0, 10.0), **kwargs):
LAMMPSBase.__init__(self, label, **kwargs)
try:
ljcut, coulcut = pair_cutoff
except:
ljcut = pair_cutoff
coulcut = pair_cutoff
self.parameters.units = 'real'
self.parameters.pair_style = 'lj/cut/coul/long %f %f' % (ljcut,
coulcut)
#self.parameters.pair_style = 'lj/cut/coul/cut %f %f' % (ljcut, coulcut)
self.parameters.pair_modify = 'mix arithmetic'
self.parameters.bond_style = 'harmonic'
self.parameters.angle_style = 'harmonic'
self.parameters.kspace_style = 'ewald/disp 0.0001'
self.ff_data = ff_data
self.type_resolver = typing.TypeResolver(clayff_types)
def __init__(self,
ff_file_path,
label='charmm',
pair_cutoff=10.0,
auto_charges=False,
**kwargs):
LAMMPSBase.__init__(self, label, **kwargs)
self.parameters.units = 'real'
self.parameters.pair_style = 'lj/charmm/coul/charmm 8.0 10.0'
self.parameters.bond_style = 'harmonic'
self.parameters.angle_style = 'charmm'
self.parameters.dihedral_style = 'charmm'
self.parameters.improper_style = 'harmonic'
self.parameters.special_bonds = 'charmm'
# Read force field file
self.ff_data = read_charmm_params.read(open(ff_file_path))
self.type_resolver = typing.TypeResolver(charmmtypes.data)
self.auto_charges = auto_charges