Shuangxing Dai wrote:
Thanks for the help.
The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat.
Do you have any idea of this information?
The Berendsen method does not produce a proper ensemble for either temperature
or pressure. If you want true NPT, use Parrinello-Rahman. This is all
documented there are numerous threads about it in the literature and in the list
archive.
-Justin
Thanks,
Shuangxing Dai
On Jul 12, 2010, at 15:43, "Justin A. Lemkul" <jalem...@vt.edu> wrote:
Shuangxing Dai wrote:
Hi, all:
I am studying thermal expansion of bulk crystal solid. I want to reach the
state with 300K in temperature and 1 bar pressure. I am not sure whether my
procedure is correct or not.
First I run energy minimization, then a constant volume for temperature
coupling ( integrator is sd), then run with Berendson for anisotropic pressure
coupling for 50 ps, then run anisotropic pressure coupling using Panello-Rahman
for 10 ps, finally a constant volume step for production for 10 ps.
I do not know whether this procedure is correct or not. Also, since for my
small system, fluctuation is very large, so is there any way to reach the state
( 300K and 1 bar) and the system is fully in equilibrium?
The timeframes you're using are extremely short. I'd suspect that it would be
hard to get any system, especially a small one prone to large fluctuations, in
an equilibrium state in 70 ps total. Simple equilibration of a protein in
water is typically done for no less than 100 ps per ensemble.
Also, I got a question about the ,mdp file options. When I use md
integrator, with Nose-Hover for temperature coupling and Panello-Rahman
pressure coupling, there is no error information. When I change and use
Berendson for pressure coupling, there is error information and does not work.
Well, what's the error? This kind of description will get you no useful advice.
The error information is: Using Berendsen pressure coupling invalidates the
true ensemble for the thermostat.
-Justin
Anyone have idea about these? Thanks in advance.
Thanks,
Shuangxing Dai
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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