[lammps-users] Hydrophobicity model

Dear Lammps users,

For implementing proper Hydrophobic interactions, I need to change slightly WCA potential. In fact, I want to change the shift parameter by (1-λ)*ε. How can I do this?

Best Regards


You have to provide a bit more context.

What “shift parameter” are you referring to?
What are the lambda and epsilon you are quoting and what is the relation to the Lennard Jones epsilon and sigma?

Dear Dr.Axel Kohlmeyer

In order to study hydrophobic interactions between amino acids in proteins, some people used the potential that I attached.
So lambda and epsilon parameters come from experimental studies. For example, for TYR-TYR interaction, sigma=6.46A, lambda=0.865 and epsilon equal to 0.2.

For that you would either need to write your own custom pair style: https://docs.lammps.org/Modify.html
or try to use pair_style table. Tabulation is a quick way to realize custom potentials, but can be challenging to get accurate results.
I strongly suggest to practice and explore how to do effective tabulation by comparing to the existing lj/cut pair style so that you can gauge what kind of errors you can incur with your choice of tabulation settings (and minimize those).