How to specify C6/C12 instead of sigma/epsilon in topologies?

User discussions
1

GROMACS version: 2021
GROMACS modification: No

Hi,

I would like to simulate a silica substrate having a complex 6-18+Buckingham potential. I managed to find what I believe is a decent approximation using only LJ with expressions:

C12r^-12 - C6r^-6

However, my C6/C12 constant are not convertible into sigma/epsilon (e.g. for a couple of atom types C12=0).

I was wondering if there is a way to specify C12/C6 instead of sigma/epsilon when specify the nonbonded parameters in .itp files.

p.s. I am assuming GROMACS can handle C6/C12 LJ potentials, but I might be wrong

2

Hi,

as I understand the manual this is done by setting combination rule to 1 in your [ defaults ] directive.

Link: Parameter files — GROMACS 2021.4 documentation

Note that this affects all interactions, so you’ll need to include your water model files etc. explicitly and change their values to equivalent C6/12.

Petter

3

Ah, I see. Thanks Petter.

It’s a bit counter-intuitive tough, since you would think that the combination rule only affects the… combination between differente atomtypes, not the way parameters are specified for each atomtype.

I don’t have any water at this point in the system, I am just trying to simulate the annealing of a silica slab; I will use another force field later when introducing water too.