[gmx-users] Graphene topology file

#SUKRITI GUPTA# SUKRITI002 at e.ntu.edu.sg
Mon Jul 7 13:55:04 CEST 2014

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?

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.

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: Monday, July 7, 2014 6:09 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Graphene topology file

On 7/7/14, 12:36 AM, #SUKRITI GUPTA# wrote:
> Hi all,
> After getting the topology file for graphene, when i tried to freeze graphene
> and do energy minimization with just water molecules around it, then the
> graphene structure becomes distorted ie. the upper layer of the graphene
> shifts down and the terminal carbons forms bond with each other. I think this
> happens because i did not add terminal hydrogens to the graphene sheet as I
> wanted periodic boundary conditions in x y direction. Also the box size in z
> direction is shown to be zero in the output file of energy minimization. Can
> anyone please let me know how to solve this problem?

If the z-dimension is zero, then your box isn't set up properly.  Likely you're
just getting clashes between periodic images.  Setting up a proper box should
solve the problem.



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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