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. Thanks and Regards Sukriti ________________________________ Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Thursday, July 10, 2014 1:26 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/9/14, 9:06 AM, #SUKRITI GUPTA# wrote: > Thanks for the reply Justin. I just checked my box size again and found it to > be smaller than the required. Hence I changed the size and ran the simulation > again. This time energy minimization happened correctly without any change in > the graphene structure. But when I am doing npt, 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 2.5A to 11A. > > Can you please help me figure out the problem. > Does the box expand along z? Are you using walls? If not, you should be, in the case of pbc = xy. -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. -- 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.