KONG Xian wrote:
Dear all:

I am working on a research to study whether the Lateral pressure profile influence the protein function.

To get different lateral pressure profile, I used Parinello-Rahman P coupling method and anisotropic pressure coupling with different p_ref values(such as 0.9bar, 1bar, 1.1bar, .,2bar) in xy.

         I wonder whether this method feasible.

If it is not feasible, could anyone please give me a hint on how to do it.


I would be amazed if you were able to determine any difference at all between such small increments of pressure. Instantaneous pressure values fluctuate on the order of 10^2 - 10^3, depending on the size of the system, so your results would be based on the assumption that 1 +/- 1000 and 1.1 +/- 1000 are somehow different. A few additional notes:

http://www.gromacs.org/Documentation/Terminology/Pressure

There's nothing to say you can't try it, but don't be surprised if the differences in response are negligible, if they exist at all. Your systems will have to be extremely well-equilibrated for the P-R barostat to give you stable pressure values.

-Justin

--
========================================

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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