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

Berk Hess gmx3 at hotmail.com
Mon Aug 10 14:53:35 CEST 2009

No, it should be exactly opposite.
I guess you must have done something wrong (forgot to run grompp or mdrun?).

Exclusions only affect non-bonded interactions.
Pair interactions do not influence and are not influenced by the exclusions section
or non-bonded interactions.


Date: Mon, 10 Aug 2009 20:38:57 +0800
Subject: Re: [gmx-users] About exclusion of non-bonded interaction for pairs 	of energy groups
From: nomadoro at gmail.com
To: gmx-users at gromacs.org

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

Lee Soin wrote:

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 

So can this conclusion be drawn: the presence of a pair interaction automatically eliminates 
the corresponding non-bonded interaction?

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Nanjing University, China

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