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leelasd/dipole_moments_mdtraj.py

Created June 19, 2015 16:01
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Static Dielectric Constant from MD_Traj
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dipole_moments_mdtraj.py
import numpy as np
import mdtraj as md
from mdtraj.geometry.thermodynamic_properties import *
import mdtraj.utils.unit.unit_definitions as u
temperature=300
traj = md.load('md_prod2.xtc', top='md_prod2.gro')
charge=np.genfromtxt('charges',dtype='f8',usecols=[0])
charges=np.tile(charge,267)
print static_dielectric(traj, charges, temperature)
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