Hi gromacs users, I read that for slab geometries where you need pbc in xy, you can use pbc=xyz and have a slab of vacuum in between the periodic images in z and use ewald3dc (Yeh and Berkowitz method). So I changed my mdp file extended my box in z direction( with no solvent molecules) and did the energy minimization and npt again. In em, the box looks fine but with npt again I get same output i.e. water molecules fly away and box size in z direction increases drastically, through the vacuum layer is still maintained. Then I changed my pressure coupling to Parinello- Rahman instead of Berendsen. This time npt runs some steps and gives an error message:
Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. Can anyone please let me know how can I solve this problem. If we have a layer of vacuum, wont the box size reduce in npt and cause this error? Should I skip npt and directly do nvt? 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 #SUKRITI GUPTA# <sukriti...@e.ntu.edu.sg> Sent: Wednesday, July 16, 2014 11:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file 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. -- 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.