On 12/5/14 10:54 PM, vg wrote:
Dear gromacs users I read the tutorial of umbrella sampling and have a small question I don't know I do a umbrella samping simulation as the tutorial show us, the pmf image also like the tutorial result . But I was read another papers like the explain paper of g-wham: JCTC 2010.6 3713-3720. The pmf image have a immediately move up in figure 1&2 。 How could I get the pmf image like this? do I need to take more window in the high energy barrier position or just use some commands behind the g-wham or modify the map file ? Look forward reply and thank you very much
I presume you mean that the energy minima are well defined with a steep increase at small values along the reaction coordinate. The tutorial example does not have such a well defined minimum because you can't physically force the protein chains any closer; it is impossible to stably sample very small values of the reaction coordinate, though an energy minimum becomes defined with sufficient sampling. The PMFs you refer to are for very simple, small molecules, which can sample short COM distances.
P.S. i take the two figure in attachment please check.
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-Justin
Your sincerely Cao China ,TianJin, Nanking university School of physics Ph.d 发自我的 iPad
-- ================================================== 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.
