[gmx-users] alchemical free energy calculation with physical PBC

[Johannes Hermann]

Dear all,

I am calculating free energy changes with the alchemical free energy 
framework provided in gromacs. My alchemical transformation involves a 
charge change in a periodic system, where the periodicity is physical in 
the bound state but "artificial" in the unbound state. I know there is a 
bunch of literature dealing with correction schemes when using PME - but 
it did not find anything when the periodicity is physical, e.g. when 
simulating a membrane. So:

What is the "error" in gromacs free energy calculation? Is it the 
Interaction with itself in the periodic image or an interaction with a 
changing neutralizing background charge which sums up? So should I try 
keeping a zero net charge over all alchemical transition windows also in 
the physical periodic setup.

Thanks and all the best

Johannes