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

**Date:** Tue Mar 02 2004 - 03:58:28 CST

**Next message:**Vlad Cojocaru: "Locally Enhanced Sampling"**Previous message:**Peter Jones: "temp coupling coefficients"**In reply to:**Peter Jones: "temp coupling coefficients"**Next in thread:**Hyonseok Hwang: "Re: temp coupling coefficients"**Reply:**Hyonseok Hwang: "Re: temp coupling coefficients"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*> just to re-ask some questions regarding temperature control which I
*

*> don't think have been answered (Satyavani Vemparala 25/2/04, Hyonseok
*

*> Hwang 24/2/04, Wei Fu 20/2/04, Hyonseok Hwang 9/2/04).
*

*>
*

*> How does one decide what value to use for the langevin coupling
*

*> coefficient (0.1, 5, 10?), or what is an appropriate value?
*

The Langevin damping coefficient determines how fast the atoms "forget" their

momentum, and how fast the lost energy is re-introduced by stochastic forces.

The bigger the coefficient, the faster temperature fluctuations are

compensated, and the farther the dynamics is from Newtonian motion (and

closer to a purely stochastic motion).

If you're interested in dynamic properties, you'll want to use coefficients as

small as possible (while still keeping the temperature reasonably constant).

For the biological systems I've simulated, values around 1 ps-1 were good

trade-offs. You should only need more if strongly exothermal phenomena happen

in your system - maybe when starting the equilibration of a new system - but

then usually you don't mind too much if temperature raises a little for a

short time.

*> Is there any relationship between the langevin coupling coefficient and
*

*> the temperature coupling coefficient in Berendsen's method?
*

I believe this question was not answered previously because it is not easy to

see what kind of relationship you are looking for. Since the algorithms are

really different, what relationship could there be between their parameters ?

Both coefficients are the reciprocal of a characteristic time of the

thermostat, and both are related to a friction coefficient, but as far as I

can see, the similarity ends there. For example, the Berendsen friction

coefficient depends on time, whereas the one in Langevin does not.

Also I'm not sure I understand what the use of such a relationship would be.

If you want a Berendsen coupling simulation and a Langevin simulation to be

equivalent, don't forget that Berendsen coupled MD trajectories do not sample

from the canonical ensemble.

Maybe someone on the list will have something to add on these points, though.

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/

**Next message:**Vlad Cojocaru: "Locally Enhanced Sampling"**Previous message:**Peter Jones: "temp coupling coefficients"**In reply to:**Peter Jones: "temp coupling coefficients"**Next in thread:**Hyonseok Hwang: "Re: temp coupling coefficients"**Reply:**Hyonseok Hwang: "Re: temp coupling coefficients"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:37:23 CST
*