No, it should be exactly opposite.
I guess you must have done something wrong (forgot to run grompp or mdrun?).
Exclusions only affect non-bonded interactions.
Pair interactions do not influence and are not influenced by the exclusions
section
or non-bonded interactions.
Berk
Date: Mon, 10 Aug 2009 20:38:57 +0800
Subject: Re: [gmx-users] About exclusion of non-bonded interaction for pairs
of energy groups
From: nomad...@gmail.com
To: gmx-users@gromacs.org
2009/8/10 Mark Abraham <mark.abra...@anu.edu.au>
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.
Actually, I added the option "-reprod" and the results are reproducible. The
results for the
above-mentioned two cases are always different. So I am very confused.
However, I believe you've merely added a second identical non-bonded
interaction between 1 and 4, so you will get different results regardless.
Then I tried to remove the two lines:
[ exclusions ]
1 4
And retained the pair interaction that I have defined. But this lead to no
difference in the
simulation result. Is it that the "exclusion" of non-bonded interaction between
atom 1 and
atom 4 didn't work?
On the other hand, in another set of simulations, I removed the pair
interaction part:
[ pairs ]
1 4 1
In this case, the presence and absence of the "exclusion" part do make a
dramatic
difference.
So can this conclusion be drawn: the presence of a pair interaction
automatically eliminates
the corresponding non-bonded interaction?
Mark
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--
SUN Li
Department of Physics
Nanjing University, China
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