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.s...@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 > -- > 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
