[gmx-users] Trouble with gmx distance

[Teemu Murtola]

The help text explains this: "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.

In other words, the selections resemble those that were earlier required by
g_bond, not those by g_dist. The wiki page on tool changes for 5.0 shows an
example if using "plus" in a selection to get the behavior of g_dist to
compute the distance between centers-of-mass of two groups.
On Jul 11, 2014 2:04 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
> Hi All,
>
> I have encountered a very annoying problem with gmx distance (the 5.0
> replacement for g_dist/g_bond) - selections must have an even number of
> atoms. Can anyone explain why this is necessary?  I designed a minimal test
> system (distance between two atoms), and got:
>
> -------------------------------------------------------
> Program:     gmx distance, VERSION 5.0
> Source file: src/gromacs/trajectoryanalysis/modules/distance.cpp (line
> 198)
> Function:    void gmx::analysismodules::{anonymous}::checkSelections(const
> SelectionList&)
>
> Inconsistency in user input:
> Selection 'first' does not evaluate into an even number of positions (there
> are 1 positions)
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Indeed, the code makes sure the selection size is a multiple of 2, but
> why?  Is there a workaround?  Not all groups are even :)
>
> -Justin
>
> --
> ==================================================
>
> 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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