On 6/14/17 5:18 PM, Mohsen Ramezanpour wrote:
Hi Justin, Thanks for your reply, Here are the outputs for EM step: Steepest Descents converged to Fmax < 100 in 5198 steps Potential Energy = -2.6418572e+05 Maximum force = 9.5666359e+01 on atom 54770 Norm of force = 5.7127428e+00 It seems okay to me. I chose the setting you mentioned. Interestingly, it also works for MD with dt=1 fs. Not for dt=2 fs, though. Based on visualization, some lipid chains are crossed which I think this cause the problem. Not sure how can I fix them.
Surprising. With such a low force, I wouldn't expect there to be any overlap or detrimental close contact. An initial equilibration with dt = 1 fs is a possibility, or a more robust method for constructing the system, whatever that may be.
-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.
