[gmx-users] on gmx make_ndx

[Justin Lemkul]

On 6/18/15 8:13 AM, Brett wrote:
> Dear Justin,
>
>
> For the on-line command " g_dist -s run.tpr -f run.xtc -n index.ndx -o
> dist.xvg", then for the ndx file, it should contain 2 group of atoms, for
> example, 1 group is r 22 & a OE2, the other group is r 137 & a NH1. In the
> single ndx file, should I name these 2 groups separately? Otherwise how does
> g_dist determine the 2 groups for distance calculation? But if in the same
> ndx file it include 3 groups, what g_dist will do?
>

The number of groups in the index file is irrelevant.  You will be prompted for 
two selections.  Choose whatever is relevant.  Hopefully you tried the command 
and got your answer in a few seconds rather than waiting all this time for my 
reply :)

-Justin

-- 
==================================================

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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