AMBER: Confusion about Langevin dymamics

From: Hayden Eastwood <>
Date: Fri, 31 Aug 2007 14:46:28 +0100

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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