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

[Lee Soin]

2009/8/10 Mark Abraham <Mark.Abraham at anu.edu.au>

>  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.
>
> 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.


Actually, I added the option "-reprod" and the results are reproducible. The
results for the
above-mentioned two cases are always different. So I am very confused.


>
>
> However, I believe you've merely added a second identical non-bonded
> interaction between 1 and 4, so you will get different results regardless.



Then I tried to remove the two lines:
[ exclusions ]
1 4
And retained the pair interaction that I have defined. But this lead to no
difference in the
simulation result. Is it that the "exclusion" of non-bonded interaction
between atom 1 and
atom 4 didn't work?
On the other hand, in another set of simulations, I removed the pair
interaction part:
[ pairs ]
 1  4  1
In this case, the presence and absence of the "exclusion" part do make a
dramatic
difference.
So can this conclusion be drawn: the presence of a pair interaction
automatically eliminates
the corresponding non-bonded interaction?




Mark
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-- 
SUN Li
Department of Physics
Nanjing University, China
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