[gmx-users] gmx distance

[Alex]

I fixed it by explicitly selecting group COMs using the syntax from here:
http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
The utility manual page destroyed my brain, to be honest. Something clearer
than

"*-select* <selection>
Position pairs to calculate distances for"

is needed. I'm sorry, but it is.

Thanks,

Alex




On Mon, Aug 3, 2015 at 4:38 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> 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
> anything.
>
>
> >
> >  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.
>
> Mark
>
>
> >
> > Thanks,
> >
> > Alex
> > --
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