[gmx-users] crystal, nrexcl

Justin Lemkul jalemkul at vt.edu
Sun Jun 1 01:21:59 CEST 2014

On 5/31/14, 6:01 PM, Chetan Mahajan wrote:
> Dear All,
> I have TiO2 crystal, in which bonds are not defined. Thus, I think "nrexcl"
> term in the [moleculetype] section of topology file would be rendered not
> meaningful at all. Any value there for nrexcl (I currently have it as 3)
> would not really matter. Could you confirm this please? I ideally I would
> not want any nonbonded interactions (even if between neighboring atoms)
> excluded at all, since I do not have any bonds.

Correct, nrexcl is totally irrelevant in this case.  You can use gmxdump on the 
.tpr file to confirm the absence of any exclusions.



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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