[gmx-users] Protein-POPC bilayer

Jianguo Li ljggmx at yahoo.com.sg
Fri Aug 17 03:14:09 CEST 2012

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.


From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, 17 August 2012, 7:26
Subject: [gmx-users] Protein-POPC bilayer


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?
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.

gmx-users mailing list    gmx-users at gromacs.org
* Only plain text messages are allowed!
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list