[gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Berk Hess]

> 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
interactions.

Berk

> > 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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