On 4/25/14, 5:37 PM, fantasticqhl wrote:
Dear Justin, Thanks very much for your reply! I guess the use of the Parrinello-Rahman barostat should not be a problem because the optimization ran successfully if I turned off the morse potential. Actually, I have already done the nvt optimization without morse potential before I moved to npt optimization with morse potential, the error was the same for nvt with morse potential. I just do not know why the morse potential was not working. Do you have some other ideas which may result in the problem? Thanks very much!
Well, Morse potentials aren't the functional form with which any of the biomolecular force fields in Gromacs were parametrized, so either (1) there's a bug that needs to be fixed or (2) you're doing something incompatible and the model physics is breaking down.
-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.
