def recalculate_LJ(self):
"""
Takes the values of the LJ_radius and LJ_depth arrays and recalculates
the LENNARD_JONES_A/BCOEF topology sections from the canonical
combining rules.
"""
AmberParm.recalculate_LJ(self)
ntypes = self.pointers['NTYPES']
acoef = self.parm_data['LENNARD_JONES_14_ACOEF']
bcoef = self.parm_data['LENNARD_JONES_14_BCOEF']
for i in range(ntypes):
for j in range(i, ntypes):
index = self.parm_data['NONBONDED_PARM_INDEX'][ntypes*i+j] - 1
rij = self.LJ_14_radius[i] + self.LJ_14_radius[j]
wdij = sqrt(self.LJ_14_depth[i] * self.LJ_14_depth[j])
acoef[index] = wdij * rij ** 12
bcoef[index] = 2 * wdij * rij**6
def recalculate_LJ(self):
"""
Takes the values of the LJ_radius and LJ_depth arrays and recalculates
the LENNARD_JONES_A/BCOEF topology sections from the canonical
combining rules.
"""
AmberParm.recalculate_LJ(self)
ntypes = self.pointers['NTYPES']
acoef = self.parm_data['LENNARD_JONES_14_ACOEF']
bcoef = self.parm_data['LENNARD_JONES_14_BCOEF']
for i in range(ntypes):
for j in range(i, ntypes):
index = self.parm_data['NONBONDED_PARM_INDEX'][ntypes * i +
j] - 1
rij = self.LJ_14_radius[i] + self.LJ_14_radius[j]
wdij = sqrt(self.LJ_14_depth[i] * self.LJ_14_depth[j])
acoef[index] = wdij * rij**12
bcoef[index] = 2 * wdij * rij**6
