[gmx-developers] Re: Coulomb decoupling?

Berk Hess hess at kth.se
Thu May 2 21:54:06 CEST 2013

This is all describes in the manual, AFAIK.

On 05/02/2013 09:44 PM, David Mobley wrote:
> Right, what I'm asking about is
> A) how exactly is this end result achieved? (The system is periodic, 
> so how is the periodicity removed for the end state?)
The periodicity of intra-molecular interactions is always removed.
These interactions are excluded from PME and added directly as listed pairs.
> B) how was it validated that it is working as it should be?
I checked this and it works.
> C) when you say, "without cutoffs", is this referring to just Coulomb 
> cutoffs or also LJ? I'm assuming just coulomb. If so, then there are 
> internal LJ interactions in the gas phase which are missing outside 
> the LJ cutoff (assuming the molecule is larger than the cutoff). While 
> these are also missing in solution, they are generally captured well 
> by the dispersion correction. In vacuum that is not the case, so 
> neglect of these could adversely affect solvation estimates, it seems 
> to me. Has this been tested? How?
LJ is treated as Coulomb, plain LJ, no cut-off.
> D) how will the use of decoupling affect dispersion corrections to the 
> energy and pressure? (Will the dispersion corrections still give the 
> correct free energy contribution in decoupling?) how has this been 
> tested, if at all?
This is the only complicating factor.
There is no correct way of using dispersion correction with decoupling.
As the intra-molecular interactions are excluded, these do not end up 
the average C6
and they do not end up in the pair count for dispersion correction.


> Thanks!
> On Thursday, May 2, 2013, Berk Hess wrote:
>     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> 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
> -- 
> Sent from my mobile device. Please pardon any unusual brevity or typos.

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