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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