[gmx-users] Distance between two specific residues

[Justin Lemkul]

On 3/17/16 12:01 AM, Abid Channa wrote:
> Dear Gromacs users, I am trying to calculate distance between two specific
> residues of active site of my protein in MD. I have made separate .index file
> of  two specific groups. Then I am trying this command " gmx distance -f
> md_0_1.xtc -s md_0_1.tpr -oav distance.xvg -select -n index.ndx -tu ns ".
> When I am selecting my residues numbers for option -select in above command.
> error  appeared that pairs are not found in your selection residues (1st
> residue "11 atoms" and 2nd residue "15 atoms" ). Kindly guide me how I
> calculate distance between two specific residues in MD.

If your index groups are named, e.g. r_1 and r_2:

gmx distance gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav distance.xvg
-select 'com of group "r_1" plus com of group "r_2"' -n index.ndx -tu ns

-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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