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
