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 <rjd...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
