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. 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: Tuesday, July 8, 2014 7:41 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/8/14, 1:23 AM, #SUKRITI GUPTA# wrote: > Hi Justin, > > Thanks a lot for your replies. I want to simulate a half cell with graphene > electrode only on one side, hence i am using pbc in only xy direction i.e. > direction of graphene sheet, so that I have a infinite size graphene sheet > with no side effects. But if I use 3D pbc then graphene sheet effect will be > there on the other side of the box also, which I don't want. > > Also if I use 3D PBC or 2D PBC, the major problem is that even after freezing > graphene sheet, after doing energy minimization, the sheet remains linear but > becomes distorted and new bonds are formed between terminal carbons. I don't > know what is the problem with my system. > That sounds like a topology problem. Using "periodic_molecules = yes" should allow for bonding across periodic boundaries, so bonds shouldn't be recognized between atoms at the "ends" of your sheet within the unit cell. Is that what you're describing? Images would help. Check the topology carefully to make sure it has been constructed properly. A correctly sized box with g_x2top -pbc should create a sensible topology. -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.
