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 made
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 really
up to you. Usually such rigor is not necessary, as often position restraints
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.
-Justin
[EMAIL PROTECTED] wrote:
Hi Lin!
I personally feel increasing the temperature in increments better than
giving sudden temperature jump to protein. Regarding temp coupling, both
have their limitations. Berendsen is a weak coupling, so can be used for
initial runs. Later you can use Nose-Hoover after the proper
equilibration is done. However, in case of Nose-Hoover, you might have
to select the tau_t carefully, or you will get very large oscillations.
PS: Others please do correct me, if I will be thinking a bit wrong
somewhere.
Cheers!
Monika
On Mon, 21 Jul 2008, Chih-Ying Lin wrote:
Hi
My system has been dealt with minimisation and the system was kept
constant at 0 K.
Then, I want to increate the temperature to 300 K using the Berendsen
thermostat.
Should I increase the temperature of the system step by step... ?
increase temp from 0 K to 50 K
51 K - 100 K
101 K - 150 K
151 K - 200 K
201 K - 250 K
251 K - 300 K seperately?
or increase temp from 0 K to 300 K at one time?
After the temperature of the system reaches 300 K, should I use
Nose-Hoover temperature coupling to keep the system at the
equliibration on 300 K?
I have read manual though.....
Thanks a lot
Lin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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