[gmx-users] Re gromacs Bug?

Justin Lemkul jalemkul at vt.edu
Sun Jul 20 18:25:27 CEST 2014

On 7/20/14, 12:16 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
> Hi Justin , i thought the same as you, that the problem is with the  NDX
> file, but i check the selection, the file and made diferente gro files, in
> order to check the atoms, and there are ok , or fine ,

Sorry to say I'm not sure what any of this means.  The proper diagnostic is to 
run gmxdump on the problematic .tpr file to find the groups that were assigned 
after running grompp.  There is a problem in your input somewhere.  Neither 
grompp nor mdrun will spontaneously create charges on an uncharged group.  The 
fact that your intra-CNT Coulombic interactions were so large indicates a 
serious index file problem and nothing else.  The tools only do what you tell 
them, and I am quite sure there is no bug here.



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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