[gmx-users] Persistence length of whole DNA molecule

mohan maruthi maruthiforram at gmail.com
Tue Jul 23 12:38:19 CEST 2013

 Thank you sir for a reply , I missed those atoms , I will try to replace
it and then do it.  The out put file contains not length but bonds, It says
average persistence length is 4.3 bonds. I do not know how to calculate
helical axis, I will try today using 3DNA and let you know.

Thank you very much,
Mohan Maruthi

On Tue, Jul 23, 2013 at 3:59 PM, rajendra kumar <rjdkmr at gmail.com> wrote:

> Hi,
> I have not used g_polystat, and I cannot say about usage of this tool. I
> observed that you missed two oxygen atoms (O3' and O5') in the backbone
> atom index.
> There are several methods for the calculation of persistence length of a
> polymer, and you may look into literature for theories. For example, you
> can also use end-to-end distance distribution or radius of gyrations. But,
> these methods are based on the assumptions, so one should be careful.
> When DNA bends, helical axis is expected to bend simultaneously. Therefore,
> I suggested to use the helical axis in the last mail. You can calculate
> helical axis of the DNA using external tools such as 3DNA and Curves+ . If
> you will be able to calculate the length of axis over which correlations in
> the tangents are lost, that length will be persistence length.
> The persistence length of the DNA is ~40-50 nm. To calculate persistence
> length is difficult for very small DNA because bending in small DNA is rare
> in simulations. You may look into the literature for the methods applicable
> to sub-persistence length polymer.
> With best regards,
> Rajendra
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