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
