[gmx-developers] Coulomb decoupling?

[Berk Hess]

Hi,

You didn't explain exactly what you are doing.
The decouple mdp options decouple the molecule to a vacuum state, i.e. 
pure Coulomb without cut-off's.

Cheers,

Berk

On 05/02/2013 07:10 PM, David Mobley wrote:
> Could I get some input on this?
>
> I have a couple of cases for rather polar molecules where decoupling 
> and annihilation give me statistical significant differences in 
> hydration free energies. The differences are not that large, but 
> significant. I'm trying to find out what's already been done to 
> validate so I know how much time/effort to spend testing to try and 
> figure out if there is a problem here.
>
> Thanks.
>
>
> On Tue, Apr 30, 2013 at 1:25 PM, David van der Spoel 
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
>     On 2013-04-30 18:02, David Mobley wrote:
>
>         Hi,
>
>         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.
>
>         Thanks!
>         David
>
>
>         --
>         David Mobley
>         dmobley at gmail.com <mailto:dmobley at gmail.com>
>         <mailto:dmobley at gmail.com <mailto:dmobley at gmail.com>>
>         949-385-2436 <tel:949-385-2436>
>
>
>
>
>     -- 
>     David van der Spoel, Ph.D., Professor of Biology
>     Dept. of Cell & Molec. Biol., Uppsala University.
>     Box 596, 75124 Uppsala, Sweden. Phone: +46184714205
>     <tel:%2B46184714205>.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
>     -- 
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>
>
>
> -- 
> David Mobley
> dmobley at gmail.com <mailto:dmobley at gmail.com>
> 949-385-2436
>
>

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