How to prevent two molecules from interacting with each other?

User discussions
1

GROMACS version: 2020 onwards
GROMACS modification: No

Hi all,

Is there any way to prevent two molecules from interacting with each other via Coulomb and LJ interactions in a standard MD simulation in the latest versions of Gromacs? Like something similar to the ‘energygrp_excl’ feature that was removed?

Thanks in advance!

2

No. And even the old energygrp_excl approach did not exclude long-range Coulomb interactions.

But why would you want to do that?

3

I plan to do some umbrella sampling simulations where I pull multiple permeant molecules (to improve the lateral sampling) through a lipid bilayer, but I don’t want the permeant molecules to interact with each other.

4

They will anyhow interact indirectly by interactions with other molecules, e.g. the lateral pressure in the membrane increases with multiple molecules in there. So fully decoupling is impossible. I would say it is even undesirable. For instance, if you don’t keep them apart all the lowest free-energy state is with all molecules on top of each other.