[gmx-users] Persistence length of whole DNA molecule

[rajendra kumar]

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