On Mon, Sep 30, 2002, dkeller_at_unm.edu wrote:
>
> Our system is very large so we are trying to hydrate just the part of
> greatest interest with a water cap, and freeze the rest. But a back -
> of-the-envelope calculation says that any time you use a water cap
> there should be a large image potential acting on any charged particle,
> due to the discontinuity in the dielectric constant at the surface of
> the cap. Worse, the image charge due to one real charged particle
> should also affect all the other real charged particles. I haven't
> seen any mention of this in the literature, and I know people use water
> caps all the time. Is there some reason why the image forces don't
> happen in AMBER (say, with TIPS3P water), or is there some trick to
> deal with them (or cancel them)?
>
As you point out, there *should* be a reaction field contribution (which is
about the same as an image charge contribution) from the polarization of the
solvent outside of the water cap. As I've written before, Amber does not do a
"good" job of implementing simulations with a water cap. This is primarily
because the key Amber developers generally don't do this sort of calculation.
Note that ignoring the reaction field could be an acceptable approximation
for some sorts of simulations, e.g. if you want to see how a ligand might
fit in an active, or where the waters should go, or what would happen to the
structure if a mutation were made, etc. Energetic questions, especially
involving electrostatics, are less likely to fall into this "acceptable
approximation" category; and artifactual results of all sorts can arise when
electrostatics is not handled in a consistent fashion.
(This is a classic "chicken and egg" question: if I avoid this sort of
simulation because Amber is not well-suited for it, and my co-developers feel
the same, how does the capability ever get incorporated? There has been some
off-and-on disucssion of how to get a reaction field capability into Amber,
but no clear plans yet. Suggestions or volunteers are welcome....)
..dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Mon Sep 30 2002 - 17:34:28 PDT
