Hi Justin, This was the command I used for both wild type and mutant. I wonder if you could think of any reason that made only the wild type have the PBC effects?
gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -ur compact Thank you, MD On Wed, Apr 11, 2018 at 9:23 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/11/18 9:22 AM, MD wrote: > >> Hi Gromacs folks, >> >> I was trying to use RMSF to compare c-alpha of a wild type and mutant in a >> 100 ns simulation. I discarded the 10-30 ns and compared them side by side >> in non-overlapping time windows of 30-40ns, 40-50ns, 50-60ns, 60-70 ns, >> 70-80 ns, 80-90 ns and 90-100ns. The RMSF of wild type and mutant overlay >> pretty well with exceptions of some regions with minor flexibility >> differences, but the c-alpha RMSF of wild type went crazy starting from >> 70-80ns (7-8 folds of a more drastic change) and lasted until the end, >> while the mutant stayed in the same range of changing. >> >> Does this mean that I should trust the simulation after 70ns, or I should >> continue the simulation and see if the system will calm down eventually? >> Any help will be appreciated. >> > > It sounds to me like one simulation isn't properly corrected for PBC > effects (protein jumping back and forth) while the other is. Make sure the > trajectory is sensible; gmx rmsf doesn't intrinsically account for PBC so > you have to judiciously apply trjconv before running the analysis. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.