[gmx-users] carbon nanotube - ifnite in length ?

Justin Lemkul jalemkul at vt.edu
Thu Oct 10 15:46:04 CEST 2013

On 10/10/13 9:39 AM, Steven Neumann wrote:
> And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] - is
> there any gmx tool to exclude interactions within the given molecule so 1
> with all 1200, 2 with all 1200...etc... 1200 with all 1200?

No, but it's a simple script to write since you just iterate through a counter. 
  Alternatively, just use a [nonbond_params] directive to set the interactions 
of the atoms to zero (unless they have charges, in which case you do need 



Justin A. Lemkul, Ph.D.
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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