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

[Lee Soin]

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. 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?
Thanks in advance.

2009/7/28 Mark Abraham <Mark.Abraham at anu.edu.au>

> Lee Soin wrote:
>
>> So there is no place to specify electrostatic interactions for pair
>> interactions?
>>
>
> No. The charges are specified in the [ atoms ] directive. Read the example
> in chapter 5.
>
>
> Mark
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-- 
SUN Li
Department of Physics
Nanjing University, China
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