[gmx-users] g_mindist on 51-frame trajectory gives 51 minimum distances but <51 atom pairs
mczwier at gmail.com
Fri Jan 27 02:49:27 CET 2012
Thanks for the reply. I'm not using the contact information at all
(-on is unspecified), and yes, it still generates a result for >6A in
the distance output (-od) , but the result for which atoms are at the
reported distance is sometimes missing from the atom pair output (-o)
On Thu, Jan 26, 2012 at 6:42 PM, Peter C. Lai <pcl at uab.edu> wrote:
> 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
>> Matt Z.
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> Peter C. Lai | University of Alabama-Birmingham
> Programmer/Analyst | KAUL 752A
> Genetics, Div. of Research | 705 South 20th Street
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