[gmx-users] Graphene topology file

#SUKRITI GUPTA# SUKRITI002 at e.ntu.edu.sg
Wed Jul 16 05:21:00 CEST 2014

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.


Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
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: Saturday, July 12, 2014 5:17 AM
To: gmx-users at 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.


I know nothing about using walls, so that's the best I can suggest.



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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