On 2/24/14, 4:22 AM, davhak wrote:
Dear All, I try to restrain the movement of a certain particle in all cholesterol molecules (coarse-grained model) in Z direction. To do this I add a [ position_restraints ] section under the [ moleculetype ] of cholesterol itp file like: [moleculetype] CHOL 1 ... [ position_restraints ] ; i funct fcx fcy fcz 8 1 0 0 100000 The problem is that during the simulation the restrained atoms already after a few hundred ns move by ~0.2 nm in average. No matter whether the restraining force constant is set to 100000 0r 1000. The log file shows that the restraining energy varies around 300-500 kJ/mol regardless of the restraining force constant value (there are over 200 cholesterol molecules in the system). As expected one gets the same outcome when the position restraint is applied according to the Gromacs manual i.e. by setting a define in the mdp file and including a separate position_restraints] itp file within an #ifdef #endif clause right after the inclusion of the cholesterol itp file. It should be something trivial missing in my understanding of how position restraint should be applied.
A restraint is an applied bias to disfavor some behavior, not completely prevent it. A net movement of 0.2 nm over hundreds of ns is not particularly large.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
