[gmx-users] on the command gmx distance
jalemkul at vt.edu
Mon May 25 18:33:57 CEST 2015
On 5/25/15 3:48 AM, Brett wrote:
> Dear All,
> Suppose I have completed a production MD, and I want to get the distance of
> OD1 of ASP204 in chain G and NH1 of ARG42 in chain A for the last 5 ns in the
> MD, will you please tell me the detailed command of gmx distance (how to
> write the input file and output file in the command) on how to get the
I'm not well versed in the new selection syntax (though it is really quite
flexible), but this is trivial to do in conjunction with the "old way" of making
index files with make_ndx and then calling gmx distance:
chain G & r 204 & a OD1
chain A & r 42 & a NH1
Then just invoke gmx distance -select "com of group x plus com of group y"
(subbing in x and y as appropriate).
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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