[gmx-users] Graphene topology file

#SUKRITI GUPTA# SUKRITI002 at e.ntu.edu.sg
Tue Jul 8 07:23:55 CEST 2014

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.



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 12:44 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Graphene topology file

On 7/7/14, 7:54 AM, #SUKRITI GUPTA# wrote:
> Hi Justin,
> Thanks for the reply. Actually I am having the problem of z- dimension to be
> zero only when I am giving pbc only in xy direction. For pbc in xyz, the z
> dimension is not becoming zero. So do you still think it can be because of
> improper box size chosen?

No, the z-dimension would not be relevant with pbc = xy.

> Also I have not given nwall option in .mdp file. As Abhijit suggested, it can
> create a problem. I do not have any idea about nwall functioning and what
> parameters to choose for it to work with xy periodic graphene sheet. I am
> unable to find any tutorial about this also. Can you please suggest me what
> to do for this.

The manual discusses walls in great detail, though they're not required in this
case.  What reason do you have for only using 2-D PBC?  Why not 3-D (pbc = xyz)?



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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