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

[Alessandra Villa]

Hi,

On Wed, Mar 18, 2020 at 4:52 PM Johannes Hermann <johannes.hermann at tum.de>
wrote:

> 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.
>
>
Yes that is always good to try to keep zero the net charge change

Alessandra



> Thanks and all the best
>
> Johannes
>
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