[gmx-users] Scaled 1-5 interactions

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jun 5 02:31:22 CEST 2009

Borys Szefczyk wrote:
> Dear GROMACS Users,
> I would like to use the OPLS force field, but with additional scaling
> factor for the Coulomb 1-5 interactions for certain atoms. More precisely,
> I want to use the standard 0.5 scaling for Coulomb and LJ 1-4 interactions
> and 0.8 scaling factor for Coulomb 1-5 interactions. Is there a way to
> do this within the topology file of Gromacs or do I need to modify the code?

I can't think of a way to do this natively. Trying to use fudge-LJ for 
1-4 and pairs for 1-5 won't work (see 5.7.1 of manual).

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.


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