[gmx-users] exclusions

Justin Lemkul jalemkul at vt.edu
Thu Dec 5 16:40:00 CET 2013

On 12/5/13 10:28 AM, Steven Neumann wrote:
> I guess I need to write [ exclusions ] as TUB is composed of other
> energygrps. I have 2516 atoms, that would be difficult to write [
> exclusions ] manually, would you recommend any script? I am not programming
> :(

It's an easy loop.  Every atom is excluded from all others.  You just need to 
take care to not write repetitive exclusions (i.e. an exclusion of 1 2 is the 
same as 2 1), but that's simple to do.

Learning a simple scripting language is an essential skill; it will save you 
countless hours.



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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