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

[Mark Abraham]

Lee Soin wrote:
> My problem is actually as follows:

Please describe in as full detail as reasonable the first time :-)

> I have three groups of atoms: A, B and C. Now I want to keep full
> interaction between A-B and A-C, but only retain the repulsive part of VDW
> interaction between B-C. I'm using the OPLS force field. It seems to me that
> the parameters for OPLS in the .itp files are specified for each atom, so is
> there any way to treat the interaction pairwise?

Yes, use [ pairs ] directives to overrride the atomtype-based lookup. 
That will be tedious if there are many such atoms. Read parts of chapter 5.

Probably, no force field was parameterized to reproduce whatever it is 
you're trying to observe.

Mark