[gmx-users] opls combination rule and pairs info

[Claudio J. Margulis]

Hi,
I am trying to use gromacs to simulate a protein and some sugar ligands 
using oplsaa.
I have the following 2 questions:

1) why is it that in ffoplsaa.itp combination rule 2 is the default when 
I believe oplsaa
has been parameterized with geometric mean not arithmetic mean?

2)I made my own itp file for the sugars with stretch bend torsions 
charges and lj parameters from a paper from tirado rives and jorgensen.
The question is the following: if I don't put a [ pairs ] entry in the 
itp file and I just specify "generate pairs yes" and the fudge factors 
to 0.5 at the beginning of the file, I do not get the same energy as if 
I put the [ pairs ] entry with all the corresponding 1,4 pairs (always 
keeping the fudge factors to 0.5).
If I run g_energy I do not even see the entry for 1-4 interactions in 
the lj and coulomb section. I thought that if you specified generate 
pairs yes, that would automatically check for the 1-4 pairs and apply 
the corresponding fudge factor.
Could you please shed light on this issue??

I know that the correct energy is being computed when i put all the 
entries in the [ pairs ] section because i have computed it 
independently from gromacs.

Thanks a lot in advance. Cheers,

Claudio.




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Claudio Javier Margulis, Ph.D.                       
Chemistry Department                               
Columbia University                                
Web http://www.chem.columbia.edu/~claudiom/        
Work phone (212) 854-8470                          
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