On 11/17/16 10:06 PM, Irem Altan wrote:
Hi, I’m trying to apply umbrella sampling to a system following Justin Lemkul’s tutorial. I’m confused about how the distances are calculated, however. When I run a pull simulation and calculate center of mass distances with gmx distance, I see that the distance in the 0th configuration is 3.003 nm. When I look at the output PMF generated with gmx wham, the PMF starts from 2.56 nm. What could I be missing?
Your sampling includes distances as low as 2.56 nm. This isn't necessarily wrong. The average in the window should match the average calculated by gmx distance, but without seeing a whole lot of steps that you left out in your description, it's impossible to know if your setup is exactly what you think it is. Confirm the reference distance that grompp prints out before the run, consider the strength of the spring constant for the restraint, etc.
-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.
