Re: [Apbs-users] apbs-users Digest, Vol 42, Issue 4

[Gernot K. <ge...@ch...>]

Hi!

On Mon, 2009-12-14 at 10:35 +0000, J.Dziedzic wrote:
> Below I'm listing the \Delta{}G values produced by your script
> along with the value of the total electrostatic energy in sdie=1,
> pdie=\epsilon, obtained after \Delta{}G to the E1 value calculated above.

Shouldn't it be sdie=\epsilon and pdie=1? Otherwise \Delta{}G would be
the solvation energy of set of point charges in a small \epsilon=80
bubble surrounded by vacuum.

> \epsilon	\Delta{}G	E in dielectric of \epsilon
> 80		-27119		-8785
> 50		-26905		-8571
> 30		-26526		-8192
> 10		-24650		-6316
> 5		-21865		-3531
> 4		-20480		-2146
> 3		-18181		153
> 2		-13606		4728
> 1		0		18334
> 
>    What is the reason for my getting negative energies? Could that
> be that the dielectric is polarizing sooo much?

Well, it would suggest that the solvation energy in absolute values is
larger than the Coulomb repulsion of your system. Sounds kind of counter
intuitive with point charges of +6 and +1 at close distance. But I have
the feeling you mixed up sdie and pdie (see above).

>    On a side note -- I thought of a simple approach to remove the grid
> artefact, can you comment on the feasibility?
> 
> 1) Output the charge distribution to an OpenDX file.
> 2) Locate all 3x3x3 pockets of isolated charge floating in a sea of
> zero charge.
> 3) Calculate the Coulomb sum for the interaction of these 27 charges.
> Since they will always be in a cavity, epsilon will be that of pdiel
> and constant. Repeat for all 3x3x3 charge pockets.
> 4) Subtract the obtained result from what APBS produces.
> 
>    This assumes that all point charges are separated by at least one
> grid point of zero charge and that chgm spl2 is used.
> 
>    Is this feasible?

Maybe. But in the end it's easier (and faster?) to simply subtract the
homogenious APBS result. If electrostatics is really time-limiting and
the grid artefact creates a serious problem in your application you
should consider using a Generalized Born approach. The currently fastest
implemention comes from the group of Prof. Caflisch:

http://www3.interscience.wiley.com/journal/116327343/abstract?CRETRY=1&SRETRY=0

and is part of the latest CHARMM version 35.

Best regards,
Gernot Kieseritzky