[gmx-users] calculation of persistence length

[Johnny Lu]

Hi. I guess g_polystat can't do that.

The online reference for gmx polystat ((
http://manual.gromacs.org/programs/gmx-polystat.html) says:
"...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?
(http://www.cenapad.unicamp.br/parque/manuais/Gromacs/online/g_angle.html)
(http://manual.gromacs.org/programs/gmx-angle.html)


On Sat, Sep 12, 2015 at 2:33 AM, soumadwip ghosh <soumadwipghosh at gmail.com>
wrote:

> 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,
> IITB
> Mumbai
> India
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