[gmx-developers] Re: Coulomb decoupling?

[David Mobley]

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?)
B) how was it validated that it is working as it should be?
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?
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?

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
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-developers-request at gromacs.org.
>
>
>
>
> --
> David Mobley
>
>

-- 
Sent from my mobile device. Please pardon any unusual brevity or typos.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20130502/de42d62e/attachment.html>