[gmx-users] Scaled 1-5 interactions

Borys Szefczyk szefczyk at mml.ch.pwr.wroc.pl
Fri Jun 5 11:31:57 CEST 2009

On Fri, Jun 05, 2009 at 10:31:22AM +1000, Mark Abraham wrote:
> Setting the number of exclusions for a moleculetype to 4, in a forcefield 
> with "generate_pairs = yes" and "fudgeLJ = 0.5" will probably see pdb2gmx 
> get everything except the 1-5 interactions right. Then you post-process the 
> .top from pdb2gmx in a (e.g.) perl script, using the [ bonds ] entries to 
> recognize 1-5 interactions (which you add as [ pairs ]). You look up the 
> normal LJ functions for those atom types, then invoking the combination 
> rule and your 0.8 scaling and write parameters on the [ pairs ] entry for 
> each 1-5 pair. grompp will then blindly eat what you give it. Such 1-5 
> interactions will be reported by mdrun in with the normal LJ interactions.

Dear Mark,

thank you for the answer. I think, I have to explain more precisely what
is the problem, because what I want to do is to scale the charges, not
the LJ parameters!

Kony et al. (JCC 23: 1416, 2002) have proposed an OPLS-AA force field
for carbohydrates. In this forcefield they scale the 1-5 and 1-6
electrostatic interactions to counterbalance the 1-4 interactions, which
are scaled by a factor of 0.5. The LJ interactions are scaled only for
1-4 pairs. They were using modified GROMOS to do the calculations.
I was wondering it this kind of modification would be possible in GROMACS.
What I understand from the manual, the pair function type 1 scales
only LJ interactions, so it will not do the trick. Table 5.4 of the
manual lists also pair function type 2 which uses fugeQQ, qi, qj, V and W,
but section 5.3.4 says that it is ment for FEP calculations, so I don't
know if I could use it for my purpose. Table 5.4 lists also another
entry called pairs_nb (which defines qi, qj, V and W), but I could not
find any explanation for it in the manual.


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  Department of Chemistry,  &  Institute of Physical & Theoretical Chemistry,
       Faculty of Science,  &  Wroclaw University of Technology
       University of Porto  &  http://ichfit.ch.pwr.wroc.pl/people/szefczyk

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