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