How can I remove a specific interaction?

User discussions
1

GROMACS version: 2026.0
GROMACS modification: Yes/No
I am currently studying ion-phospholipid interactions, specifically, I want to see how cations interact with carbonyl groups, but in the MD simulations I’ve performed, most of the interactions occur between the phosphate group and the cation. Can I reduce the intensity/frequency of this interaction, and if so, how can I do it?

2

You should not modify interactions because you don’t see what you want to see. But the force field used might be not be sufficiently accurate. In particular cations can be difficult to parametrize. Have you checked the literature for validation of the combination of phosphate and cation force field you are using?

In GROMACS you can not modify interactions between specific atoms. You can modify Lennard-Jones interactions between specific atom types. Likely the cation interactions with a specific atom type in the phosphate, so then you can modify that interaction specifically.

3

Thanks for your reply. I have now looked into literature and, based on what I have read, I should use a polarizable forcefield like Drude instead of an additive forcefield. I cannot find much information on how to use it though, is there any user guide out there I haven’t seen?

Thanks a lot

4

I would think one should be able to get a sufficiently accurate force field with polarizability. But then the force field should be specifically parametrized to correctly reproduce the interactions you are interested in.

Adding polarizability for a single group, like an ion, is relatively easy.