[gmx-users] Protein-POPC bilayer

[Mark Abraham]

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?

Mark