Re: AMBER: Confusion about Langevin dymamics

From: David A. Case <>
Date: Fri, 31 Aug 2007 07:53:47 -0700

On Fri, Aug 31, 2007, Hayden Eastwood wrote:
> How can you be certain of molecular time scale events if the bulk water
> being modelled over-estimates the viscosity of the surrounding medium?

You can't. If time scales are of interest to you (as they often are to me)
you should not use Langevin or any other thermostat, since all temperature
regulation interrupts Newtonian dynamics.

A typical friction term for Langevin simulations (say of gamma_ln = 5) is only
10% of the true solvent friction. So, if you do use a Langevin thermostat
with explicit solvent, the dynamics won't be all that wrong because of double
counting. Izaguirre, Skeel, and co-workers haverecommended using Langevin
coupling with even smaller friction constants, and you might want to study
some of those papers, e.g.:

%A J.A. Izaguirre
%A D.P. Catarello
%A J.M. Wozniak
%A R.D. Skeel
%T Langevin stabilization of molecular dynamics
%J J. Chem. Phys.
%V 114
%P 2090-2098
%D 2001

[Aside: if you are interested in molecular time scales, you should also
carefully consider which water model you use, since popular ones are often
rather poor in modeling the viscosity of actual water.]

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Received on Sun Sep 02 2007 - 06:07:32 PDT
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