Dear Sir, Thanks for the useful insight.
On Fri, Apr 26, 2013 at 2:21 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > Average coordinates are problematic and not generally representative. > Consider for instance the average coordinates of a methyl group connected > to X. The rotation around the C-X bond causes the average positions of the > hydrogens to line up. Consider using g_cluster to find representative > structures from your trajectory. > > Erik > > On 26 Apr 2013, at 06:59, bipin singh <bipinel...@gmail.com> wrote: > > > Thanks for your reply. > > Actually I am interested to see how much structural deviation is > occurring > > in a protein during the simulation from its average position of atoms > > rather than the initial position (crystal structure or starting > structure). > > The motivation of doing this analysis is the fact that in real solution > > phase, a system may not be static and if we consider the time average > > structure of a simulation to be the real representative of the structure > in > > solution phase rather than static crystal structure. > > > > > > > > > > > > > > > > On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > > > >> Hi Bipin Singh, > >> > >> That indeed gives you the RMSD against the average. Do think about it a > bit > >> more: do you want the average of the whole structure, or should you > account > >> for a phase of relaxation? > >> > >> Cheers, > >> > >> Tsjerk > >> > >> > >> On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> > >>> > >>> > >>> On 4/24/13 3:06 AM, bipin singh wrote: > >>> > >>>> Hi all, > >>>> > >>>> Please let me know whether this is the right way to calculate RMSD > from > >>>> the > >>>> average structure from a simulation: > >>>> > >>>> g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg > >>>> > >>>> > >>>> average.pdb: is the pdb file produced using -ox option of g_rmsf. > >>>> > >>>> > >>> You can calculate RMSD with respect to whatever structure you like, but > >>> the interpretation and justification for doing so are up to you. > >>> > >>> -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< > >> 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< > >> http://lists.gromacs.org/mailman/listinfo/gmx-users> > >>> * Please search the archive at http://www.gromacs.org/** > >>> Support/Mailing_Lists/Search< > >> 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< > >> http://www.gromacs.org/Support/Mailing_Lists> > >>> > >> > >> > >> > >> -- > >> Tsjerk A. Wassenaar, Ph.D. > >> -- > >> 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 > >> > > > > > > > > -- > > *----------------------- > > Thanks and 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 > -- *----------------------- Thanks and 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