[gmx-users] distance between two groups

[Justin Lemkul]

On 6/7/16 8:12 PM, Qasim Pars wrote:
> Dear gmx users,
>
> How can I calculate the distance between the central of mass of two groups
> ( for example: ligand and protein)? As far as I understand gmx mindist does
> not do it.
>

This is what gmx distance does.  The exact syntax is given in an example on 
http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0#g_dist

> And is that possible to calculate the distance per residue as a function of
> time? I would like to calculate the distance between ligand and each
> residue as a function of time.
>

Invoke a series of calls to gmx distance with appropriate index groups. 
Otherwise, to get the time-average, you can use gmx mdmat, but that will be an 
average minimum distance, not an average COM distance.

-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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