[gmx-users] Replica exchange: Coordinates and simulation box size?

[Daniel Burns]

Hi Johannes,

Somebody please correct me if I'm wrong but I believe it is just the
thermostats that are exchanged.

A given simulation box's velocities are rescaled accordingly after the
exchange and the simulation continues with its own fluctuations in box size
assuming it is pressure-coupled.

I don't know anything about incorporating free energy calculations with
replica exchange though.

Aloha,

Dan

On Mon, Mar 23, 2020 at 11:07 AM Johannes Hermann <johannes.hermann at tum.de>
wrote:

> Dear all,
>
> I have slightly different Position Restrains and Box sizes over my
> lambda windows in an alchemical Free Energy Calculation in NVT ensemble
> (I know that my calculated Free Energy Difference will not solely depend
> on the mutation alone..)
>
> What happens if I use replica exchange? What exactly is exchanged within
> different windows: Only the coordinates or also the current simulation
> box size?
>
> Thanks in advance!
>
> All the best
>
> Johannes
>
>
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