Thanks a lot Sanku for your help. On Thu, Nov 1, 2012 at 11:38 PM, Sanku M <msank...@yahoo.com> wrote:
> Bipin, > There might be a workaround. You might want to check out Plumed plugin > in latest versions of VMD for calculating fractions of native contact. You > can load the gromacs trajectory along with the native .gro file in VMD and > use Plumed plugin inbuilt in VMD . You need to install plumed most probably > early. > > > > ________________________________ > From: bipin singh <bipinel...@gmail.com> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Thursday, November 1, 2012 1:23 PM > Subject: Re: [gmx-users] fraction of native contacts calculation > > Thanks for your response. Hope to see this feature in upcoming GROMACS > release. Before that, could it be possible to get the modified code in the > user contribution section, it may be useful for many GROMACS users. > > > On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund <er...@xray.bmc.uu.se> > wrote: > > > > > 31 okt 2012 kl. 13.43 skrev Justin Lemkul: > > > > > > > > > > > On 10/31/12 6:02 AM, bipin singh wrote: > > >> Hello all, > > >> > > >> Is there any way to calculate fraction of native contacts during the > > >> simulation in gromacs. I searched the archives but didn't found any > > >> significant clue. > > > > > > At present, there is no way to do this. Likely one could modify the > > g_mindist code to do this - it would be a very nice feature. > > > > > > > If one could get the -sel option of g_hbond to work again then you would > > get such information with -contact. > > > > Erik > > > > > > > -Justin > > > > > > -- > > > ======================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Research Scientist > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > jalemkul[at]vt.edu | (540) 231-9080 > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > ======================================== > > > -- > > > 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 > > > > ----------------------------------------------- > > Erik Marklund, PhD > > Dept. of Cell and Molecular Biology, Uppsala University. > > Husargatan 3, Box 596, 75124 Uppsala, Sweden > > phone: +46 18 471 6688 fax: +46 18 511 755 > > er...@xray.bmc.uu.se > > http://www2.icm.uu.se/molbio/elflab/index.html > > > > -- > > 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 > > > > > > -- > ----------------------- > *Regards,* > Bipin Singh > -- > 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 > -- ----------------------- *Regards,* Bipin Singh -- 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