Re: AMBER: Confusion about Langevin dymamics

From: Carlos Simmerling <>
Date: Fri, 31 Aug 2007 09:52:02 -0400

Langevin dynamics is usually used with implicit solvent.
Even then there are issues; for example, real solvent viscosity
depends on solvent exposure and is anisotropic, while neither
is taken into account in Amber's implementation.
If used with explicit solvent, it is a good idea to use low viscosity for
the reasons that you state.

On 8/31/07, Hayden Eastwood <> wrote:
> Dear AMBER users
> I have puzzled for some time about the Langevin equation and I wonder if
> anyone can answer this question for me:
> Why does the Langevin equation possess a frictional coefficient?
> I am simulating a protein in explicit solvent and it seems to me that the
> explicit water particles already give rise to a "frictional" term. Thus,
> it
> appears that there are 2 origins of friction when employing Langevin
> dynamics; that of the actual bulk water, and that of the imaginery bulk
> water (ie that which is implicit to the langevin equation). Surely, this
> "double counting" of friction just slows phase space sampling and is
> otherwise needless? Furthermore, does this not adversely affect comparison
> with some experiments, since the "double" friction term inevitably means
> that phase space sampling is "slower" than the experimental reality. Ie.
> How
> can you be certain of molecular time scale events if the bulk water being
> modelled over-estimates the viscosity of the surrounding medium?
> Many thanks
> Hayden Eastwood
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Received on Sun Sep 02 2007 - 06:07:30 PDT
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