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

Justin A. Lemkul jalemkul at vt.edu
Tue Dec 1 23:45:58 CET 2009

t.peter.Mueller at gmx.net wrote:
> 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

Can you post some of this output?

> 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.

Is this for the CA-only trajectory?

> 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.

Before we jump to the bug conclusion, can you post the command line you're 
using, groups you're selecting (are they custom? simply the default "C-alpha"?) 
and relevant snippets from the output and/or coordinate files that demonstrate a 
bit better what's going on.  If, based on this information, things look weird, 
then file a bugzilla with files that reproduce the problem.  I would disagree 
that g_mindist requires bond information, since a .tpr file is not strictly 
required for its function.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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