[gmx-users] Monitor distance between atoms

[Justin Lemkul]

On 8/27/14, 2:01 PM, Eric Smoll wrote:
> Hello Gromacs Users,
>
> Is there a way to output the distance between and atom X and all atoms
> within distance R of atom X along a trajectory?
>
> I am paging through the manual but I can't seem to find anything like this.
>
> I would settle for the coordinates of all atoms within a distance R of atom
> X along the trajectory as well.
>

gmx distance should be able to do both of these tasks.  Some notes on syntax 
changes since the pre-5.0 g_dist:

http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0#g_dist

-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 601
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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