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.

--Jianguo



________________________________
From: Shima Arasteh <shima_arasteh2...@yahoo.com>
To: Discussion list for GROMACS users <gmx-users@gromacs.org> 
Sent: Friday, 17 August 2012, 7:26
Subject: [gmx-users] Protein-POPC bilayer


 Hi,

I have a question about the Protein-POPC system:
To insert a protein in lipid bilayer, I am suggested to simulate POPC in water 
separately before insertion, it might decrease the time of final simulation. 
It's OK!

In the article suggested me by dear Peter C. Lai, I read that POPC was 
simulated in anisotropic pressure coupling at first and then after insertion of 
protein, semi-isotropic pressure coupling is applied. 
Now, would you please telling me why you used this procedure?
And,
Would my system be correct  if I use semi-isotropic pressure coupling instead 
of anisotropic pressure coupling for the first step?

Thanks in advance for your replies.


Sincerely,
Shima
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