[gmx-users] How to exert different lateral pressure profile of a membrane to study its influence on a protein inserted in the double layer membrane?

[Justin A. Lemkul]

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

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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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