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
