Strange behaviour or behave as designed?

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1

GROMACS version: 2019
GROMACS modification: Yes/No
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Used mindist function with -on -or to generate contacts and distance by residues.
Index file includes two groups

  1. lipid type1 (with one specific atom)
  2. res1 res2 (with one specific atom)

Then the mindist was run in following sequences:-
e.g. 1st group Lipid-type1, 2nd group Res1 Res2
Then used the same function by reversing the groups
e.g. 1st group Res1, Res2 2nd group lipid-type1

In my understanding the number of contacts for both of these should be the same.
But the results shows it is not the case.
e.g. in first set, the number of contact between the specific lipid and residues are 10 over trajectory. (that’s very low).
in the second set, the number of contacts between residues and lipid is over 1000 over the same trajectory.

Can someone please let me know what’s going on here, why am I getting two different values for the same set of residues?

2

I think the manual page of gmx mindist explains this.

3

hi hess, thanks for your reply

I have read it many times, I don’t follow a place that indicates such.
can you please explain to me what I am not getting here?