from IPython.display import Image
import os, sys
import __main__
__main__.pymol_argv = [ 'pymol', '-cp' ]
import pymol 
pymol.finish_launching() 
from pymol import cmd

%%bash
trjconv -f b_md.xtc -s b_md.tpr -o b_md.pdb -skip 20 -pbc mol

%%bash
cd servalli

%matplotlib inline
import numpy
import matplotlib.pyplot as plt
s=numpy.loadtxt("box_1.xvg")
t=s[:,0]
x=s[:,1]
z=s[:,3]
ar=x*z/32
print t
plt.plot(t,ar)
plt.show()

%matplotlib inline
s=numpy.loadtxt("sas_b.xvg")
t=s[:,0]
fob=s[:,1]
fil=s[:,2]
print t
plt.plot(t,fob)
plt.plot(t,fil)
plt.show()