On 1/11/14, 11:50 AM, Andres Ortega wrote:
Hi, Dear Gromacs Users I was running de Umbrella Sampling Tutorial, and when i get the frames from the trajectory, there are some frames like this: 489 5.3776196 490 5.3817739 491 5.3752654 492 5.3619911 493 5.3890083 494 5.3918220 495 5.4115819 496 5.4074620 497 5.4386061 498 5.4179682 499 5.3942749 500 5.3905423 is this ok? , they shouldn´t be always move away from the other molecule ?
This is perfectly fine. At this COM distance, there is no appreciable interaction between the reference and pulled groups, so the pulled group mostly just diffuses randomly at this point. Remember that the spring is pulled with constant velocity, but the pulled species only responds to both this applied force and the forces within the system, which at this point are just collisions with the solvent.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. 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 ================================================== -- 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.
