GROMACS version: 2021.3
GROMACS modification: No
Here post your question
I have a very basic question on parameterization of non-bonded parameters (LJ) of atoms. The target system is a cluster/aggregate of metal atoms.
From experimental data, I can get the atomic radius and vdw radius of the atoms. However, looking at the LJ parameters (epsilon and sigma) of metal atoms in INTERFACE FF, these donot agree. For example, the atomic radius of silver atom is 0.14 nm and vdw radius of 0.17 nm. However, INTERFACE FF has r0 of 0.29 nm (and epsilon 4.56 kcal/mol) (https://pubs.acs.org/doi/10.1021/jp801931d).
I was wondering if there is a way to calculate r0 from atomic/vdw radii. Or, do these LJ parameters need to be empirically derived. If latter is the case, is there a detailed tutorial on how to arrive at these parameters from trial simulation runs.