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

[Mark Abraham]

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

>>> 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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