[gmx-users] Protein-POPC bilayer
jalemkul at vt.edu
Fri Aug 17 03:46:34 CEST 2012
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users