On 4/7/15 7:11 AM, Ming Tang wrote:
Hi, Justin I am working with a triple helix using umbrella sampling method. When generating configurations, I pulled 1ns (md_pull.mdp). Then I got 15 configurations using 0.03 spacing. They are conf0.gro conf5.gro conf10.gro conf15.gro conf17.gro conf18.gro conf30.gro conf31.gro conf39.gro conf59.gro conf87.gro conf161.gro conf233.gro conf360.gro conf488.gro. Most of the configurations are within 0-100 frames. Does this affect the umbrella sampling simulations? Is there any pulling time requirement when generating the configurations? I was supposed to have a try and find the result, but found that the calculation is time-consuming. So I decided to ask you finally.
The physics of every system is different. It's hard to generalize. If you have configurations that allow for reasonable window spacing, the quality of the end result depends on the sampling and convergence of the umbrella sampling itself.
-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.
