On 7/16/14, 10:58 AM, Timothy Click wrote:
I added the -alldih, readjusted the parameters to match the desired distances, etc., and if I don’t freeze anything, I receive the following error upon a minimization attempt. Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 There were 4490 inconsistent shifts. Check your topology WARNING: Listed nonbonded interaction between particles 6 and 48 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason.
There's something fundamentally wrong, but I'd be guessing at what that is at this point. If you package up your (1) coordinates, (2) topology (.top and any necessary .itp files), (3) force field files, and (4) .mdp files into a tarball and post them somewhere for download, I will take a look at this later today.
-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.