[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
Justin A. Lemkul
jalemkul at vt.edu
Tue Jul 22 05:46:00 CEST 2008
I too rely heavily on the Berendsen methods for T- and P-coupling, and have
always found them satisfactory. I have not seen much beyond the casual
references to the fact that N-H T-coupling and Parrinello-Rahman P-coupling are
superior in terms of membrane simulations. I have tried both, and have found
both setups to be equally reasonable in their results. It seems, overall, that
Nose-Hoover schemes are often applied using NAMD and CHARMM software. I don't
know if this choice is motivated by the software, or the force fields used.
There are a few casual references to Berendsen being less than optimal in the
literature and in archived presentation materials (which I can probably unearth
if I can recall my Googling :).
Based on experience, I too would agree that Berendsen suffices, and only made
mention of the N-H argument as a talking point, something that others have argued.
If I come across any of these references again, I will be sure to post them to
the list to continue the discussion.
chris.neale at utoronto.ca wrote:
> Hi Justin,
> I wonder if you could expand upon the following statement, or perhaps
> offer some links or references.
> "Some argument can be made that N-H is more applicable to membrane
> I am interested because I use a Berendsen thermostat for membrane
> simulations. To be entirely honest, I have no particular understanding
> of the consequence of this choice beyond the oft-heard statement that
> Berendsen T-coupling doesn't yield the correct ensemble. But it is very
> intuitive and, as you say, it's usage is quite common and I have thus
> far relied on these points to guide my choice of temperature-coupling
> algorithm. Therefore I am hoping to take advantage of this opportunity
> to learn a bit more about temperature coupling as you seem to understand
> it quite well.
> I am hoping that you can outline the logic underlying the 'correct
> ensemble' statement and indicate how this is especially applicable to
> membrane simulations.
> I do realize that this is a large request on this type of mailing list.
> Please feel free to decline.
> Much obliged,
> -- original message --
> I have used the Berendsen method almost exclusively in my simulations,
> and it is
> widely used in most of the literature I read. While the argument can be
> that Nose-Hoover gives a result closer to the true ensemble than
> Berendsen, I
> think both are sufficient for simple protein in water simulations. Some
> argument can be made that N-H is more applicable to membrane simulations.
> As for whether or not you need to slowly increase the temperature, it is
> up to you. Usually such rigor is not necessary, as often position
> are applied to the protein during initial equilibration. I have never
> experienced any adverse effects of simply setting the initial temperature,
> although that's not to say it's not possible :)
> Just my $0.02.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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