[gmx-users] FEP calculation with charged species

[Александр Лашков]

Good afternoon. I calculated the FEP for the ligand-water system and the
ligand-protein-lipid bilayer to calculate the free binding energy. I have a
ligand with a total charge of +1. Rocklin et al (2013) described
corrections for periodic boundary conditions in the case of Ewald
summation. However, they either do not introduce counter ions there at all,
or compensate  only the charge of the protein and consider the case of
protein in water. In my initial FEP calculation, the compensating charge
balances the ligand charge too. How equivalent is the case described in the
article? Can I apply article calculations directly to my case or is it
better not to make electrostatic corrections at all?
I calculated the values of the ligand solvation energy in the ligand-water
system in the absence and in the presence of counterions and obtained
similar results. It turns out that the corrections described in the article
act in the same way in the case of the initial charge compensation by
counterions and in the absence of such compensation?
Alex