Hello Sir, Thank you very much for a reply. I have selected following atoms P, C5',C4',C3' atoms to estimate persistence length. I want to find persistence length of whole dna, can you please elaborate on , how to calculate persistence length of whole dna using helical axis of the dna?
Thanks & regards, Mohan On Mon, Jul 22, 2013 at 3:35 PM, rajendra kumar <rjd...@gmail.com> wrote: > 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 > -- 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