(x, y, z) = coordinates[index]
positions[index, 0] = x
positions[index, 1] = y
positions[index, 2] = z
positions = Quantity(positions, angstroms)
# Load forcefield
forcefield = ForceField(
get_data_filename('forcefield/smirnoff99Frosst.ffxml'))
# Define system
topology = generateTopologyFromOEMol(mol)
params = forcefield.getParameter(smirks='[#1:1]-[#8]')
params['rmin_half'] = '0.01'
params['epsilon'] = '0.01'
forcefield.setParameter(params, smirks='[#1:1]-[#8]')
system = forcefield.createSystem(topology, [mol])
"""
paramlist1 = np.array([100.,140.,60.,140.,60.])#np.arange(float(sys.argv[2]),float(sys.argv[3]),float(sys.argv[4]))
paramlist2 = np.array([109.5,76.5,76.5,142.5,142.5])
#j = sys.argv[5]
smirkseries = '[*:1]~[#6X4:2]-[*:3]'#sys.argv[6]#'[#6X4:1]-[#1:2]'
paramtype1 = 'k'#sys.argv[7]#'length'
paramtype2 = 'angle'#sys.argv[8]
param = forcefield.getParameter(smirks=smirkseries)
for i,j in zip(paramlist1,paramlist2):
param[paramtype1] = str(i)
(x, y, z) = coordinates[index]
positions[index, 0] = x
positions[index, 1] = y
positions[index, 2] = z
positions = Quantity(positions, angstroms)
# Load forcefield
forcefield = ForceField(
get_data_filename('forcefield/smirnoff99Frosst.ffxml'))
# Define system
topology = generateTopologyFromOEMol(mol)
params = forcefield.getParameter(smirks='[#1:1]-[#8]')
params['rmin_half'] = '0.01'
params['epsilon'] = '0.01'
forcefield.setParameter(params, smirks='[#1:1]-[#8]')
system = forcefield.createSystem(topology, [mol])
smirkseries1 = sys.argv[2]
eps = sys.argv[3]
rmin = sys.argv[4]
epsval1 = sys.argv[5]
rminval1 = sys.argv[6]
smirkseries2 = sys.argv[7]
epsval2 = sys.argv[8]
rminval2 = sys.argv[9]
param1 = forcefield.getParameter(smirks=smirkseries1)
param1[eps] = epsval1
param1[rmin] = rminval1
