Re: [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 
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.
> 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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[gmx-users] calculation of persistence length

[soumadwip ghosh]

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.
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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