Re: AMBER: collision frequency in GBSA dynamics

From: David A. Case <>
Date: Tue, 25 Jan 2005 14:23:34 -0800

On Tue, Jan 25, 2005, Giulio Rastelli wrote:
> I am running a molecular dynamics calculation on a protein structure using GBSA
> (igb=5, gbsa=1) using amber8. Using Langevin dynamics (ntt=3) one need to se
> the collision frequency (gamma_ln) to something different from the default of
> zero...what value of gamma_ln would be "appropriate" for this gb calculation?

The friction term for water is close to 50 ps^-1, but it is generally
advantageous to use a much smaller value, say 5 -10. You should be aware that
no value really is a good approximation to the *dyanmics* of a water system,
but values around 5 generally do a good job of sampling the configurations
one expects for a solvated room temperature simulation.

Take a look at this paper:

%A R.J. Loncharich
%A B.R. Brooks
%A R.W. Pastor
%T Langevin dynamics of peptides: The frictional dependence of isomerization
rates of N-actylananyl-N'-methylamide
%J Biopolymers
%V 32
%P 523-535
%D 1992

....good luck...dac

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Received on Tue Jan 25 2005 - 22:53:00 PST
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