Dummy Alchemical Ions in Gromacs

GROMACS version: 2024.1



I have been working on calculating protein-protein relative binding energies using De Groot’s Double-System Single-Box setup (Mutation free energy calculations and https://doi.org/10.1021/acs.jctc.0c01045).

The idea is the following:
You generate an alchemical path between the wild type and the mutant type of the mutant protein using pmx, simulate the forward and reverse simulation paths, and then you perform a FEP to get a ∆∆G from which you can get the free binding energy.

De Groot implements this in a Double System Single Box Approach to preserve the charge of the system upon mutation if the residues have different charges. This works

The problem is that this implementation makes the system much larger. I noticed openMM has an alchemical ion concept that can have a changing charge along the alchemical path (changes with lambda), and this effectively solves the problem by ensuring that the system is always neutral.

Can I use a virtual ion in Gromacs to have the functionality similar to the alchemcial ion in openMM, meaning that I change the charge of the ion to keep a neutral charge in the system?