On Sun, Dec 15, 2013 at 1:42 PM, xiao <helitr...@126.com> wrote: > Dear all, > > I am doing a MD on a mutant protein which is unstable from exprient. > However, i found no difference between the wild type and the mutant protein > from md, the structure and the rmsd are very similar in the mutant and the > wild type. > > Can anyone tell me how to tackle this problem? > > It depends on a large number of factors. When you say the protein is unstable, does it ever actually fold? Does it fold into a metastable state? How has stability been determined experimentally, and most importantly, over what time frame? If you're talking differences in half-life of even seconds, you'll never see that via MD. The exact approach is also a function of the force field and its inherent caveats or deficiencies and the sampling in your simulation. Are you doing one simulation and hoping to see a difference, or are you running multiple simulations/conducting REMD?
-Justin -- ========================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ========================================== -- 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.