Re: AMBER: Are the constant pH simulations with explicit water possible?

From: David A. Case <>
Date: Tue, 29 Mar 2005 09:37:27 -0800

On Tue, Mar 29, 2005, Kateryna Miroshnychenko wrote:

> I'm going to perform constant pH simulations in AMBER8.
> As far as I've understood this can only be done with implicit water
> representation. Why couldn't I treat water explicitly?
> Is that because unit cell must be neutralized? And why should it be
> neutralized?

The need for implicit solvent has nothing to do with neutralization of the
unit cell. In implicit solvent, adding a proton leads to an instantaneous
response of the "solvent" to the new charge distribution. This would not
happen with explicit solvent, and the procedure used in Amber to sample
protonation states would not work well with explicit solvent.

There will be a review of constant pH methods (using both explicit and
implicit solvent) in the April issue of Curr. Opin. in Structural Biology.
That may give you a clearer idea of various possibilities that have been

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Received on Tue Mar 29 2005 - 18:53:00 PST
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