On 5/3/15 1:17 AM, mah maz wrote:
Dear all, I need to freeze some atoms in my system not to move during simulation. I used freezegrps and freezdim options but after simulation, I can see that the fixed atoms also moved and their coordinates changed. What can I do to fix their positions? Should I couple them with thermostat and assign low temperatures to avoid their motion?
Either your frozen groups are set up incorrectly or you're looking at the wrong atoms. What does gmx traj report about the coordinates of the atoms in those groups?
-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.
