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calc_table.py
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Sun, May 12, 07:27

calc_table.py
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#!/usr/bin/env python
# Calculate a table of pairwise energies and forces between "INT" atoms
# in the lipid membrane model described in
# Brannigan et al, Phys Rev E, 72, 011915 (2005)
# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
def U(r, eps, sigma):
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
def F(r, eps, sigma):
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
epsilon = 2.75/4.184 # kCal/mole
sigma = 7.5
Rmin = 0.02
Rmax = 22.6
rcut = 22.5
N = 1130
for i in range(0,N):
r = Rmin + i*(Rmax-Rmin)/(N-1)
U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
F_r = F(r, epsilon, sigma)
if r > rcut:
U_r = 0.0
F_r = 0.0
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))

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