[gmx-users] Protein-POPC bilayer
jalemkul at vt.edu
Fri Aug 17 04:33:04 CEST 2012
On 8/16/12 10:21 PM, Mark Abraham wrote:
> On 17/08/2012 11:46 AM, Justin Lemkul wrote:
>> 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.
> Or depends on the force field or lipid?
Certainly a possibility. I think that the statement in the manual makes it
pretty clear though that the algorithm itself is likely responsible for at least
some of the observed deformations - "Beware that anisotropic scaling can lead to
extreme deformation of the simulation box."
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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