[gmx-developers] Coulomb decoupling?
David van der Spoel
spoel at xray.bmc.uu.se
Tue Apr 30 22:25:51 CEST 2013
On 2013-04-30 18:02, David Mobley wrote:
> In GROMACS 4.6 and later, there's now a new feature available to allow
> decoupling of solute molecules in free energy calculations. I wanted to
> inquire as to how Coulomb decoupling works, as I'm not clear.
> Specifically, imagine I'm running a calculation of the hydration free
> energy of a small molecule in water, and I decouple it (LJ and Coulomb)
> from its surroundings. What is the final reference state for the small
> molecule? Is it the small molecule interacting with periodic copies of
> itself in the gas phase (bad)? Or is it not interacting with periodic
> copies of itself either? If the latter, how is this achieved?
Good question, also one would like to be able to decouple a molecule
only in the central box and not in the surrounding boxes. This does not
make a difference for liquids but it does for crystals.
> Since I'm not familiar with the Coulomb decoupling aspect and it is
> conceptually more complicated than LJ decoupling, I want to make sure I
> understand how it's supposed to be working.
> David Mobley
> dmobley at gmail.com <mailto:dmobley at gmail.com>
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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