[gmx-users] Persistence length calculation using g_polystat

[Mohan maruthi sena]

Hello Sir,
                Thank you very much for a reply. I have selected following
atoms P, C5',C4',C3'  atoms to estimate persistence length. I want to find
persistence length of whole dna,  can you please elaborate on , how to
calculate persistence length of whole dna using helical axis of the dna?



Thanks & regards,
Mohan


On Mon, Jul 22, 2013 at 3:35 PM, rajendra kumar <rjdkmr at gmail.com> wrote:

> Which group of atoms you have taken for the persistence length? g_polystat
> requires a group of atoms which are consecutively bonded in polymer
> main-chain. You should take only backbone atoms of one strand of the DNA.
> But, it does not give the persistence length for the whole DNA. I guess, to
> estimate persistence length of whole DNA, you have to calculate it for
> helical axis of the DNA.
>
> With best regards,
> Rajendra
>
> |================================================|
> |* Rajendra Kumar                                 *|
> | PhD Student                                    |
> | Max Planck Institute for Biophysical
> Chemistry<http://www.mpibpc.mpg.de/english/start/index.php>
>  |
> | Theoretical and Computational
> Biophysics<http://www.mpibpc.mpg.de/home/grubmueller/index.html>,
>      |
> | Am Fassberg 11, 37077 Goettingen, Germany      |
> | Tel.:  +49 551 201 2304                        |
> |================================================|
>
>
> On Sun, Jul 21, 2013 at 11:27 PM, Mohan maruthi sena <
> maruthi.sena at gmail.com
> > wrote:
>
> > Dear gmx users,
> >                           I would like to calculate persistence length of
> > DNA using gromacs command g_polystat . The out put file of persists.xvg
> > contains  persistence length in number of bonds and it shows that the
> > average persistence length = 4.3 bonds.  How can we convert no of bonds
> in
> > to length(nm)?. Please suggest me a way to solve this.
> >
> >
> > Thanks for a reply in advance,
> >
> >
> > With regards,
> > Mohan
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