[gmx-users] g_mindist on 51-frame trajectory gives 51 minimum distances but <51 atom pairs

Peter C. Lai pcl at uab.edu
Fri Jan 27 00:42:57 CET 2012

I have not read the source, but the default search radius for mindist is
6A. If you have no contacts within 6A of the atoms in the primary group
to the target group for a given frame, will it still generate a result,
since for all intents and purposes the array search should be null in
that case?

On 2012-01-26 12:32:15PM -0500, Matthew Zwier wrote:
> Hi all,
> I'm running g_mindist (from 4.5.5) on a slew of very short
> trajectories (51 frames) in order to obtain both minimum distances and
> the corresponding atom pairs, using
> echo 10 11 | g_mindist -nice 10 -f seg.xtc -n $NDX -s $TPR -nopbc -o
> mindist_pairs.out -xvg none
> where NDX and TPR are (valid) index and topology files, respectively,
> and nopbc is specified because there is no periodic box (these are
> GB/SA simulations).  This is on a 64-bit Linux box, with GROMACS and
> all dependencies compiled with GCC.  For all trajectories, the
> resulting mindist.xvg always contains 51 entries with reasonable
> values (in the 1.1-1.5 nm range), but for a subset of the
> trajectories, the corresponding mindist_pairs.out contains less than
> 51 entries (as low as ~30 in some cases).
> Reading the source for gmx_mindist.c, it appears that this should
> never occur, at least not without giving a nonsense value of the
> minimum distance for that frame in the process (1 mm, it would appear
> from the source!).  I'm either missing something in my reading of
> gmx_mindist.c, I've found a bug (unlikely), or I've managed to
> convince GCC to mis-compile g_mindist somehow (more likely, though
> still somewhat baffling).  Can anyone help me figure out what's going
> on?
> Cheers,
> Matt Z.
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Peter C. Lai			| University of Alabama-Birmingham
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