[gmx-users] gmx distance

Mark Abraham mark.j.abraham at gmail.com
Tue Aug 4 00:38:50 CEST 2015


On Tue, Aug 4, 2015 at 12:19 AM Alex <nedomacho at gmail.com> wrote:

> v. 5.0.5
> I need to calculate the distance between COMs of two groups (both in index
> file) as a function of time. I can't think of anything simpler.
>  I'm doing:
> "gmx distance -f traj.trr -n index.ndx -oav dist.xvg" and then selecting my
> groups manually from the menu.

Note that you haven't said anything to gmx distance about using COM of

>  I am getting:
> "Selection 'DG' does not evaluate into an even number of positions (there
> are
> 33 positions)"
> To this effect, the manual states something that could have easily come out
> of Donald Trump:
> "gmx distance calculates distances between pairs of positions as a function
> of time. Each selection specifies an independent set of distances to
> calculate. Each selection should consist of pairs of positions, and the
> distances are computed between positions 1-2, 3-4, etc."
> It is my understanding that the distance is calculated not as the distance
> between COMs (which is only one pair), but something else.

Like it says, each selection consists of pairs of positions, and each
selection is independent of each other. gmx distance doesn't guess that
your pair of selections should be combined into a pair of positions, in one
case via forming a COM :-)

> I want the
> distance between the COM of my DG and one other group.

gmx help distance notes the existence of -selrpos, which might help here (I
don't know whether it does). Lots more background info on selections at gmx
help selections.

> Anything I am missing in the supplied options?

gmx pairdist in the 5.1 release candidate might be more helpful.


> Thanks,
> Alex
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