From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Tue Mar 02 2004 - 15:39:24 CST
Le mardi 2 Mars 2004 20:18, Hyonseok Hwang a écrit :
> Thank you very much, Jim. Your answer is very helpful. Now I
> understand them more clearly.
You're welcome. My name is Jerome, though. even if Jim certainly has to be
acknowledged for all the useful information he posts on this list.
> Could you let me know any references on Langevin temperature control
> method used in NAMD, please?
I don't have any references at hand, but I can develop a bit more here, since
it isn't too complex.
When doing Langevin dynamics, NAMD adds two forces to those deriving from the
force field :
* a frictional force, equal to - mass * gamma * velocity (gamma is the damping
coefficient)
* a stochastic force, that is normally distributed with zero average and a rms
value sigma.
As I said previously, the frictional term constantly drains the system's
kinetic energy, while the stochastic force gives back a certain amount of
energy.
To use this as a thermostat, the force rms, sigma, has to be adjusted using
the fluctuation-dissipation theorem. In this case, the FDT yields :
sigma = sqrt( 2 * kT * gamma * mass / delta_t), where delta_t is the timestep.
So NAMD uses the value of gamma provided by the user and computes accordingly
the value of sigma that will lead to the desired temperature. You can see
that if gamma is very small, sigma will be small too, so that the overall
Langevin force will be negligible compared to "physical" ones from the force
field.
All this is likely to be explained with much detail in nonequilibrium
statistical mechanics books.
Cheers,
Jerome
-- Jérôme Hénin Equipe Dynamique des Assemblages Membranaires Université Henri Poincaré / CNRS UMR 7565 B.P. 239 54506 Vandoeuvre-lès-Nancy Cedex Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 71 http://www.edam.uhp-nancy.fr/ In principio creauit Linus Linucem
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