On 6/14/17 5:23 PM, Mohsen Ramezanpour wrote:
I have done equilibration for almost 45 ns or even 60 ns for one test system. I expected with this energy and this equilibration time, it works fine. But it fails. I will construct the systems as you suggested to see what I get.
With such a long equilibration, there's no reason it should fail with dt = 2 fs if the clashes have been eliminated, because I would expect they should be gone after a few ps. I'd suspect something else in the topology or .mdp file but you'll have to do a more thorough diagnosis (e.g. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System)
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
