[gmx-users] Protein-POPC bilayer
jalemkul at vt.edu
Fri Aug 17 03:19:39 CEST 2012
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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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