[gmx-users] Gromacs and graphene sheets

Justin Lemkul jalemkul at vt.edu
Sun Jul 13 16:50:20 CEST 2014

On 7/13/14, 12:33 AM, Dr. Timothy Click wrote:
> Greetings from Taiwan. I am attempting to simulate a sugar with a graphene
> sheet in Gromacs 4.6.5. I made the grapheme sheet using VMD, which does not
> number the carbons according a bond order. However, Gromacs seems to expect
> this (e.g., 1 bonded to 2, not 1 bonded to 15). I realize that I will have

What leads you to expect that Gromacs requires such ordering?  When building a 
topology for graphene, one normally uses g_x2top, which decides bonds solely 
based on interatomic distance, not the order of appearance in the coordinate file.

> the grapheme sheet as fixed atoms, but this configuration seems to toy with
> the energies. I have even tried to use pdb2gmx with a PDB that had CONECT
> statements without success. I am using Gromacs 4.6.5, the Charmm 36 force

CONECT statements are ignored by most (all?) Gromacs programs.

> field, water, and ions. A simple minimization without constraints causing the
> grapheme sheet to become unbounded and begin with ugh energies (10E8
> kJ/mol).

This suggests an incorrectly built topology.

> I have thought about switching to Gromacs 5.0, but I don't know whether this
> problem could be solved by the switch. Any suggestions will be appreciated.

Unlikely.  Something is more fundamentally wrong, but without the exact sequence 
of commands you're using, and evidence of output that suggests what the problem 
might be, it's impossible to provide any useful help.



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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