Berk Hess wrote:
Date: Mon, 10 Aug 2009 20:52:31 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] About exclusion of non-bonded interaction for pairs
of energy groups
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.
That is incorrect.
The exclusion line makes Gromacs excluded non-bonded interactions
between atoms 1 and 4. The [ exclusions ] section, although itself
"bonded" in some ways, has no relation at all with any other bonded
interactions.
True, 5.4 does point out that there are (in a sense) two kinds of
exclusions, viz "The exclusions for bonded particles are generated by
grompp for neighboring atoms up to a certain number of bonds away, as
defined in the [ moleculetype ] section in the topology file (see
5.7.1).". Then the second paragraph goes on to point out the purpose of
[ exclusions ]: "Extra exclusions within a molecule can be added
manually in a [ exclusions ] section."
Perhaps the wording of this description could be improved, since the
sense of "[ exclusions ]" is actually "[ extra_exclusions ]"? A sentence
clarifying this before the full explanation would make things clearer:
"Exclusions
Additional pairs of particles from which non-bonded interactions are to
be excluded may be indicated under this directive. Some exclusions for
bonded particles may be generated by grompp for neighbouring atoms...
Such extra exclusions within a molecule can be added manually in the [
exclusions ] list. Each line..."
Mark
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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