Lee Soin wrote:
Hello!
Sorry to bother you again, but I have another question. I have written a
topology file of two water molecules to test the pair interaction. Here is
part of my topology file:
[ moleculetype ]
SOL 2
[ atoms ]
1 opls_116 1 SOL OW 1 -0.82
2 opls_117 1 SOL HW1 1 0.41
3 opls_117 1 SOL HW2 1 0.41
4 opls_116 2 SOL OW 2 -0.82
5 opls_117 2 SOL HW1 2 0.41
6 opls_117 2 SOL HW2 2 0.41
[ settles ]
1 1 0.1 0.16330
4 1 0.1 0.16330
[ exclusions ]
1 2 3
2 1 3
3 1 2
4 5 6
5 4 6
6 4 5
[ exclusions ]
1 4
[ pairs ]
1 4 1
I have also changed the fudgeLJ and fudgeQQ to 1.0.
Originally, there is no pair interaction in this system. First I did a
simulation when the last 4 lines were removed, that is, I treated all the
interactions as non-bonded interactions.
Since there is no bonded interaction between 1 and 4, your second [
exclusions ] directive will not have any effect. Read section 5.4.
Exclusions are cancellations only of interactions between bonded atoms.
Then I added the last 4 lines
to specify the normal non-bonded interaction between atom 1 and 4 as pair
interaction in order to see whether that will affect the result. It turns
out that the results for the two cases are different. So did I miss
something, or are pair interactions and non-bonded interactions treated
differently by GROMACS?
mdrun is only reproducible if you tell it that you want it to be with
"mdrun -reprod". So it is possible that your observation of different
results is not (yet) meaningful.
However, I believe you've merely added a second identical non-bonded
interaction between 1 and 4, so you will get different results regardless.
Mark
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