[gmx-users] calculation of persistence length

soumadwip ghosh soumadwipghosh at gmail.com
Sat Sep 12 08:33:23 CEST 2015

Dear all,
            I want to calculate the persistence length of a single stranded
DNA in the presence of various salts. I want to plot a lnP(theta) vs
1-cos(theta) graph, where theta is the bend angle of the DNA and  P(theta)
is the angular probability. From GROMACS what I obtained was as follows-

# This file was created Thu Sep  3 07:02:19 2015
# by the following command:
# g_polystat -f mdfinal_60ns.xtc -s mdfinal_60ns.tpr -p persist_18mm.xvg
# g_polystat is part of G R O M A C S:
# GRoups of Organic Molecules in ACtion for Science
@    title "Persistence length"
@    xaxis  label "Time (ps)"
@    yaxis  label "bonds"
@TYPE xy
     0.000   0.4025
     2.000   0.4472
     4.000   0.4527
     6.000   0.4958
     8.000   0.4444
    10.000   0.5157
    12.000   0.5164
    14.000   0.5471
    16.000   0.5090

Here, the time evolution of some bonds are given. Can anyone help resolving
the issue?

Thanks in advance,
Soumadwip Ghosh
Research Fellow,

More information about the gromacs.org_gmx-users mailing list