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. Thanks, MD -- 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.
