[gmx-users] on the command gmx distance

[Justin Lemkul]

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
> distance?
>

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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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