Dear Justin, Thanks so much for your help. I am still unable to solve the problem of blowing up of the box. Once I am able to do correct simulation I will update here.
Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 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: Saturday, July 12, 2014 5:17 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/11/14, 5:42 AM, #SUKRITI GUPTA# wrote: > Hi Justin, > > Thanks for the reply. I changed define= -dflexible to -dposres_water and > removed freeze graphene group in my .mdp file and ran the energy minimization > and npt again. This time for pbc= xyz, the water doesn't fly away but the > graphene sheet curves and does not remain in xy plane. Is it ok for the sheet > to bend during simulation and will it not effect the pbc? > Applying pressure along the plane of the sheet can cause deformation. Whether or not this is physically relevant, I have no idea. > Also for pbc=xy, the same problem persists as the previous one i.e. following > error occurs: > > 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. > > Can you please suggest what can be causing the error to occur? > That's a generic error suggesting the system is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System I know nothing about using walls, so that's the best I can suggest. -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.
