[gmx-users] Protein-POPC bilayer

[Justin Lemkul]

On 8/16/12 9:43 PM, Jianguo Li wrote:
> What I think is that anisotropic coupling may be faster in equilibrium. Suppose
> the protein is quite different in x and y dimensions, after  insertion, I think
> it is faster to get equilibrium the box length separately. I agree with you that
> semi-isotropic coupling in the first step can also do the job, but I expect it
> may take longer time to reach equilibrium.
>

What I generally see is basically the opposite.  Using anisotropic pressure 
coupling leads to a steady change in box dimensions, but this is not the case 
with semiisotropic coupling.  It depends, I suppose, on how one produces the 
membrane protein system - adequate deletion of lipids can accommodate for a 
protein of any shape without affecting box vectors.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
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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