In [3]:

    

import MDAnalysis
import matplotlib.pyplot as plt
import numpy as np
%matplotlib inline


    

In [4]:

    

def Rgyr(u):
    """This function will plot Radius of gyration for a give universe (trajectory)
    :input
        universe: A universe with both PSF and DCD Files.
    :return 
        1) matplotlib object for figure. 
        2) array with data. 
    """
    Rgyr = []
    protein = u.select_atoms("protein")
    for ts in u.trajectory:
       Rgyr.append((u.trajectory.time, protein.radius_of_gyration()))
    Rgyr = np.array(Rgyr)

    print Rgyr
    ax = plt.subplot(111)
    ax.plot(Rgyr[:,0], Rgyr[:,1], 'r--', lw=2, label=r"$R_G$")
    ax.set_title("Radius of Gyration")
    ax.set_xlabel("Time (ps)")
    ax.set_ylabel(r"radius of gyration $R_G$ ($\AA$)")
    #ax.figure.savefig("Rgyr.pdf")
    plt.draw()
    return  ax, Rgyr


    

In [7]:

    

trj = '50_frame.dcd'
top = './41wl_ff.psf'
u = MDAnalysis.Universe(top, trj)
fig, Rgyrdata = Rgyr(u)
#np.savetxt("SimAnaRep-RoG.data", Rgyrdata)
#fig.figure.savefig("SimAnaRep-RoG.pdf")


    

    




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 [  0.14666463  14.5950319 ]
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 [  0.63554673  14.43235824]
 [  0.68443494  14.46688002]
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 [  0.78221136  14.41274683]
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 [  0.87998778  14.38424011]
 [  0.92887599  14.41613229]
 [  0.9777642   14.56441881]
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 [  1.4666463   14.48549566]
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 [  1.61331093  14.50795497]
 [  1.66219914  14.54129607]
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 [  1.85775198  14.59042283]
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 [  1.9555284   14.45130122]
 [  2.00441661  14.5705463 ]
 [  2.05330482  14.66729859]
 [  2.10219303  14.51986238]
 [  2.15108124  14.54526494]
 [  2.19996945  14.4653264 ]
 [  2.24885766  14.46804386]
 [  2.29774587  14.5561452 ]
 [  2.34663408  14.39166516]
 [  2.39552229  14.48221981]]