[gmx-users] Persistence length calculation using g_polystat

rajendra kumar rjdkmr at gmail.com
Mon Jul 22 12:05:06 CEST 2013

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 Kumar                                 *|
| PhD Student                                    |
| Max Planck Institute for Biophysical
| Theoretical and Computational
| 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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