GROMACS version: 2024.1
Hello,
Background:
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
Problem:
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.
Question:
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?