[gmx-users] About exclusion of non-bonded interaction for pairs of energy groups
gmx3 at hotmail.com
Mon Aug 10 13:09:17 CEST 2009
> Date: Mon, 10 Aug 2009 20:52:31 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at 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
> > 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.
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