g_mindist writing bogus information in atom-pairs file when -or is invoked
I used g_mindist analysis as follows:
g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg -or res_mindist.xvg
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
g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg
Comparing mindist.xvg from both scenarios shows no difference (files
I suspect there is some bug whenever the -or flag is invoked. Strangely enough, it affect the .out file.
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,
#3 Updated by Shay A over 9 years ago
Created an attachment (id=463)
Example for g_mindist under gromacs 4
Below I give the list of files, and exact commands I used to help recreate the situation.
In both cases (gromacs 3.3.3 and 4.0.x) The atompairs files do not match (the middle column is wrong).
I have included the following files (input and output) for your inspection:
- grom4sample.gro sample gro file of the system (time = 0ps).
- grom4sample.xtc sample xtc file, 1ns simulation
- topol.top Topology of the system
- index.ndx Index file of the system. I used group number 1 (Protein) and 12 (EIC) for the demonstration.
(WITH -or flag)
g_mindist -f grom4sample.xtc -s grom4sample.tpr -n -o atompairs_with_or.out -od gmindist_with_or.xvg -or res_with_or.xvg
OUTPUT file names
g_mindist -f grom4sample.xtc -s grom4sample.tpr -n -o atompairs_NO_or.out -od gmindist_NO_or.xvg
OUTPUT file names
The atom-pairs shown in atompairs_with_or.out are incorrect. I did the same for gromacs 3.3.3. ( the link for the gromacs 3.3.3 example is: http://ibis.tau.ac.il/hemi/1nsgrom333.tar.gz ).
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#4 Updated by Shay A over 9 years ago
Created an attachment (id=464)
example for g_mindist under gromacs 3.3.3.
This is an example of input/output I made for gromacs 3.3.3. The occurrence here is the same: The middle column of the atompairs.out file is wrong if you include the -or flag, and correct if you do not.