[gmx-users] on gmx make_ndx

[Justin Lemkul]

On 6/18/15 1:08 AM, Brett wrote:
> Dear All,
>
>
> In http://www.gromacs.org/@api/deki/files/198/=gmx-tutorial.pdf, there is
>
>
>
> make_ndx -f run.gro
> At the prompt, create a group for GLU22 with “r 22”, ARG137 with “r 137”, and then
> “q” to save an index file as index.ndx. The distance and number of hydrogen bonds
> can now be calculated with the commands
> g_dist -s run.tpr -f run.xtc -n index.ndx -o dist.xvg
>
>
> Here for g_dist, it is the distance between GLU22 and ARG137, does it mean the distance between the center of GLU22 and the cnter of ARG137? If so how does GROMACS determine the center of a residue? If I want to get the distance between one specific atom of GLU22 (for example OE2) and one specific atom of ARG137 (for example NH1), how do I specify the residue and the atom of the residue together in the make_ndx ?
>

g_dist calculates center-of-mass distances.

Making index groups of single atoms is easy in text editor (just write the atom 
number you want) or with make_ndx syntax (type 'help' at the prompt to see 
examples), e.g.

r 22 & a OE2

-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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