[gmx-users] using two different combination rules for the LJ potential

Ana West awest5 at emory.edu
Wed Jul 22 21:49:23 CEST 2009


I am trying to simulate a system composed of two different molecules.   
I made the topology files for each of the two molecules and I did some  
tests to validate the force-field parameters for my system. I do have  
all the correct parameters for my system but it turns out that for the  
two types of molecules I must use two different combination rules of  
the LJ potential (the combination rule 1 and the combination rule 3).

I did some tests using Gromacs and it seems that I can specify the directive
  [ defaults ] only one time. The manual seems to indicate that I  
might be able to do something about the combination rules by including  
a [ nonbond_params ] section in an *.itp file. However, I don;t seem  
to understand the effect of the  [ nonbond_params ] directive onto the  
[ defaults ] directive normally found in the *.itp file. It seems to  
me that there is no combination rule specified in the under the [  
nonbond_params ] section. Could someone please explain to me how this  

In addition/alternatively, does anyone have any suggestions on how I  
could go about creating a successful set of topology files using two  
different combination rules for the LJ potential?

Thank you very much for your kind consideration,

Ana West
Emory University, U.S.A

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