dear Justin thanks for your replyThe plot of the RMSD against time for the trajectory generated with g_rms shows a maximum RMSD about 0.195 nm. I set cut-off value to 0.2 nm for g_clusters command. Is it a appropriate value?Sincerely.On Tuesday, September 30, 2014 2:17 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/30/14 3:36 AM, Mahboobeh Eslami wrote: > hi GMX users > i have simulated the protein-ligand complex by gromacs for 20ns. > The average for the final structure of 18 to 20 nanoseconds has been > achieved.is minimization for the final average structure required?Sincerely. > An average structure might be totally unphysical. Energy minimization of an unphysical structure leads you to something that is probably useless. I'd suggest doing clustering if you're interested in the predominant conformation(s) during a certain time period of the simulation. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
