[gmx-users] distance between two groups

[Teemu Murtola]

To calculate the distances from your ligand to multiple residues, a much
better way than a loop over multiple gmx distance calls would be to use gmx
pairdist, which should be able to calculate the distances you want in one
go.

Teemu

On Wed, Jun 8, 2016, 03:35 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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