[gmx-users] g_mindist , trajectory only CA atoms, to small values?

t.peter.Mueller at gmx.net t.peter.Mueller at gmx.net
Tue Dec 1 23:33:12 CET 2009

Dear Shay, dear Gromacians

>For purposes of debugging this bug you can also use
>the flag of g_mindist that gives out atom pairs and
>see which atom pairs is it that gromacs thinks are
> less the 1 angstrom.
I used the  "-o  atm-pair.out" option to get the atom pairs with the minimal distance.
For the all atom trajectory the correct atom pairs are selected. But for the CA trajectory the wrong atom pairs are selected.
Instead of the pairs with the shortest distance a much further pair is selected. Although the output pair from "atm-pair.out" has a distance of more then 100 Angstrom the value in  the file "mindist.xvg" is smaller then one Angstrom.

I think the "g_mindist" command has a bug. In the trajectory each residue is only represented by a single CA atom (to reduce storage footprint and increase speed), can it be that g_mindist requires that the atoms have to "connected" (no broken bonds)?
But for calculating the minimal distance of two groups this should really not be required.

Sarah Kreuz, die DSDS-Siegerin der Herzen, mit ihrem eindrucksvollen           
Debütalbum "One Moment in Time". http://portal.gmx.net/de/go/musik

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