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.
-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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