[gmx-users] Protein-POPC bilayer

[Justin Lemkul]

On 8/16/12 9:14 PM, Jianguo Li wrote:
> After inserting the protein, the equilibrium box length in the x and y dimension should be different, so you need anisotropic pressure coupling during the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so you can use semi-isotropic method.
>

Most pre-equilibrated bilayers have (roughly) equivalent x and y box dimensions. 
  Why do you think they should inherently be different?

In my experience, anisotropic coupling leads to major deformations in the x-y 
plane, taking a bilayer that is initially a square (roughly) in the x-y plane 
and turning it into a rectangle.  I'd be very curious to hear Peter's answer to 
this question.  I used to use anisotropic coupling, but now I use semiisotropic 
exclusively.

-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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