[gmx-users] calculation of persistence length
johnny.lu128 at gmail.com
Sun Sep 13 10:21:47 CEST 2015
Hi. I guess g_polystat can't do that.
The online reference for gmx polystat ((
"...the persistence length is defined as number of bonds where the average
cos reaches a value of 1/e."
The number of bonds is one number.
I don't think it is possible to recover the many cos(theta) used to
calculate this number of bonds.
How about g_angle?
On Sat, Sep 12, 2015 at 2:33 AM, soumadwip ghosh <soumadwipghosh at gmail.com>
> 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,
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