[gmx-users] RDF

[Justin Lemkul]

On 7/11/17 11:41 AM, Pandya, Akash wrote:
> Hi,
> 
> I want to calculate the RDF between a specific residue and a ligand molecule in my simulation box. Is this possible and do I have to make a special index group for that? If so how would I go about doing that?
> 

By using make_ndx or a suitable command-line selection when running gmx rdf (see 
gmx help selections, but make_ndx is often much easier to use/comprehend for 
very simple cases like this).

-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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