[gmx-developers] different nb parameters for inter and intramolecular interactions

[Berk Hess]

Lubos Vrbka wrote:

>> You could use tabulated LJ potentials.
>> If you really only have two types of interactions
>
> well, to describe my potential - it's intended (mostly) for use with 
> zeolites and their interaction with water. in the simulation, water is 
> the only "molecular" species that has interactions with itself. 
> zeolite and ions are just a collection of charged spheres interacting 
> via coulomb and buckingham potentials.
> > you can fill the dispersion table with the one and the repulsion
> > table with the other Buckingham potential and then set the c6 and
> > c12 parameters appropriately.
> could you please be more specific at this point? i'm afraid i didn't 
> get  it. if you could point me to some manual or similar thing, it 
> would be very useful.

In Gromacs there are user tables, which are described in the manual.
Normally you would use the two LJ user  tables for dispersion and repulsion
respectively. But you can (mis)use them by filling each of them with a
complete interaction function, for instance a Buckingham potential.
You than still have the C6 and C12 parmeters to make linear combinations
of these tables.
For only O-H you could use the first table and set C6 for the intermolecular
interactions. And use pair interactions for the intramolecular interactions
where you can use the second table and only set C12.

But you might also need Buckingham for the zeolite interactions.
In that case you will need the CVS code, which has many more
functionality in this respect. (the mdp_opt.html in CVS describes
this).

Berk.