On 7/10/14, 1:29 AM, #SUKRITI GUPTA# wrote:
Hi Justin, I did simulation 2 times, once with PBC in xy with walls and other time with pbc in xyz. For pbc in xy with walls with following wall parameters: nwall = 2 wall_type = 12-6 wall_density = 5 5 wall_atomtype = opls_995 opls_996 wall_r_linpot = 1 wall_ewald_zfac = 3 Energy minimization runs fine but npt shows following errror and is terminated: Step 20: The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X distance out of cell -0.290927 New coordinates: 2.411 2.006 0.982 Old cell boundaries in direction X: 0.000 2.702 New cell boundaries in direction X: 0.000 2.702 ------------------------------------------------------- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors For pbc in xyz, both energy minimization and npt run but the water is suddenly moving far away from the graphene sheet any tries to agglomerate together causing the box size to increase drastically. It is almost like the box is about to explode. Its size changes from (2.70200 2.55300 4.00000) to (11.46117 10.82915 16.96695). The box expands in x,y and z all directions.
Without full .mdp files and some images demonstrating what's going on, it's too hard to guess at what's happening here.
-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.
