On 10/8/16 2:46 PM, Alex wrote:
Dear gromacs user, In a PMF simulation of a short peptide on solid surface, I am using the "direction-periodic" as "pull-coord1-geometry" in the Z direction, then as you know the equilibration of the system in NPT ensemble is not doable for the individual windows. So, for each windows of umbrella sampling, I am going to do minimization and NVT equilibration and then MD production. I was wondering if the lack of the NPT equilibration would not badly affect on the result PMF? If so, how can I compensate it somehow?
All you're doing is sampling under a different ensemble. There's no reason to think that a PMF requires an NPT ensemble.
-Justin
By the way, I nicely minimized. equilibrated (both NVT and NPT) and a 60 ns of production simulation of my initial system before coming to the pulling step. Thanks. Regards, Alex
-- ================================================== 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.
