**From:** Jérôme Hénin (*jerome.henin_at_uhp-nancy.fr*)

**Date:** Tue Mar 02 2004 - 15:39:24 CST

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Le mardi 2 Mars 2004 20:18, Hyonseok Hwang a écrit :

*> Thank you very much, Jim. Your answer is very helpful. Now I
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*> understand them more clearly.
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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
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*> 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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