On 11/18/13 2:36 AM, Archana Sonawani-Jagtap wrote:
Hi, I am simulating a peptide in TFE-water system. I am getting following error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out o f the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. below is my em.mdp file integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 50000 nstlist = 1 ns_type = grid rlist = 1.2 coulombtype = PME rcoloumb = 1.2 rvdw = 1.2 pbc = xyz Please help me. Why this error has ocurred and what parameter should I change to resolve it.
Likely the cutoffs are simply wrong, but you haven't said what the force field is. The other possible sources of problems during EM are (1) bad topology or (2) unreasonable starting configuration.
-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.org_gmx-users mailing list firstname.lastname@example.org https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists