[gmx-users] Graphene topology file

#SUKRITI GUPTA# SUKRITI002 at e.ntu.edu.sg
Wed Jul 9 15:07:05 CEST 2014

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 Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459)
Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Tuesday, July 8, 2014 7:41 PM
To: gmx-users at 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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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