**From:** Hyonseok Hwang (*danggi_at_northwestern.edu*)

**Date:** Tue Mar 02 2004 - 13:18:22 CST

**Next message:**Fangqiang Zhu: "Generating novel structure"**Previous message:**Fangqiang Zhu: "Re: Locally Enhanced Sampling"**In reply to:**Jérôme Hénin: "Re: temp coupling coefficients"**Next in thread:**Jérôme Hénin: "Re: temp coupling coefficients"**Reply:**Jérôme Hénin: "Re: temp coupling coefficients"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Thank you very much, Jim. Your answer is very helpful. Now I

understand them more clearly.

Could you let me know any references on Langevin temperature control

method used in NAMD, please?

Thanks again.

-Hyon

Jérôme Hénin wrote:

*>>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
*

*>
*

*>
*

**Next message:**Fangqiang Zhu: "Generating novel structure"**Previous message:**Fangqiang Zhu: "Re: Locally Enhanced Sampling"**In reply to:**Jérôme Hénin: "Re: temp coupling coefficients"**Next in thread:**Jérôme Hénin: "Re: temp coupling coefficients"**Reply:**Jérôme Hénin: "Re: temp coupling coefficients"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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