[gmx-users] g_mindist -or inconsistencies with atom-pairs

shayamra at post.tau.ac.il shayamra at post.tau.ac.il
Tue Dec 22 14:30:13 CET 2009

Dear Gromacs users,

We used g_mindist analysis as follows:
g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg -or  

and surprisingly in the atom-pairs.out only several atoms in one  
residue (from group 1) were at minimum distance from group 2  
throughout the entire simulation. Checking this output manually showed  
it to be incorrect.
res_mindist.xvg seems to hold the correct data.

When running the same analysis, only omitting the -or flag, we get a  
*correct* atom-pairs.out.
g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg

Comparing mindist.xvg from both scenarios shows no difference (files  
are identical).

Is the -or flag supposed to affect the other output files of the  
g_mindist function?

Supplementary details:
1. The same thing happened when g_mindist -s was supplied with either  
.gro, .pdb or .tpr files.
2. Index-groups 1 and 2 consisted upon full molecules with no  
ommisions (full protein and not only C-alpha).
3. We ruled out PBC by using -nopi
4. This is common with the following Gromacs versions: 3.3.3., 4.0.5, 4.0.7.


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