[gmx-users] Gromacs and graphene sheets

Justin Lemkul jalemkul at vt.edu
Wed Jul 16 13:54:19 CEST 2014

On 7/16/14, 3:43 AM, Timothy Click wrote:
> Thanks for the reply and the helpful suggestion, Justin. I have now used g_x2top, changed the necessary parameters to match the CHARMM36 cgenff (graphene carbon as CG2R61). When I run a minimization with the graphene sheet defined as a freeze group, I receive the following error:

What was your exact g_x2top command?

> WARNING: Listed nonbonded interaction between particles 6 and 48
> at distance 3f which is larger than the table limit 3f nm.
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
> This, of course, leads me to believe that I have an issue with the [ pairs ] section of the topology file created by g_x2top. The pairs are defined with a function of 1.

The fact that a pair interaction is failing is not indicative of pairs being 
wrong, merely that the forces those atoms are experiencing are causing them to 
badly distort.

> My system topology file looks like this:
> ; Include forcefield parameters
> #include "charmm36.ff/forcefield.itp"
> #include "/home/tclick/research/gra/gra.itp"
> #include "/home/tclick/research/bglc/top/glucan.itp"
> #include "/home/tclick/research/dma/single/dma.itp"
> ; Include chain topologies
> ;#include "topol_Other.itp"
> ;#include "topol_Other2.itp"
> [ system ]
> ; Name
> Sugar between grapehene bilyaer
> [ molecules ]
> ; Compound        #mols
> Graphene            2
> Glucan              1
> DMA               6005
> #ifdef POSRES
> #include "posre_gra.itp"
> #include "posre_bglc.itp"
> #endif

This #ifdef block will have no effect, as it comes after the system-level 



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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