[gmx-users] gmx mdmat calculation of heavy atoms of two side chains

[Justin Lemkul]

On 7/31/17 1:19 AM, Мижээ Батсайхан wrote:
> Dear gmx users,
> 
> I would like to know about the hydrophobic interaction between heavy atoms
> of side chains in different chains of peptides. How can I use mdmat tool
> for this calculation? I  separately indexed all heavy atoms but mdmat use
> only one index group in the calculation. I re-integrated all separate
> groups into a group. Calculation result came out only two side chain
> distance image.

A single, merged group is the proper approach.  This is the only way to get a 
matrix of all (NxN) atomic interactions.

-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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