[gmx-developers] Coulomb decoupling?

[David Mobley]

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>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>
>> 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.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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-- 
David Mobley
dmobley at gmail.com
949-385-2436
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