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

Berk Hess gmx3 at hotmail.com
Mon Aug 10 14:32:41 CEST 2009 



> Date: Mon, 10 Aug 2009 22:11:57 +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
> 
> Berk Hess wrote:
> > 
> > 
> >> 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.
> 
> 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
> 

The phrase "The exclusions for bonded particles" is indeed confusing.
I now replaced it by:
The exclusions for non-bonded interactions are generated by grompp...

I also added a few more words in this section to clarify things.

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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> > 
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