[gmx-users] Placing a peptide at the air/water interface

Sun Nov 4 17:51:28 CET 2007

Hi Mark,

I am so sorry, but I erased your mail before reading it. So, could you please send the mail one more time? It is important to me.

Thank you very much


-----Original Message-----
From: "OZGE ENGIN" <OZENGIN at ku.edu.tr>
To: gmx-users at gromacs.org
Date: Sun, 04 Nov 2007 13:36:02 +0200
Subject: [gmx-users] Placing a peptide at the air/water interface

Hi all,

I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface. 

I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in order to center the peptide. I expect to place the peptide at interface. However, instead of placing it at interface, the center of the box is changed its old values. 

How can I place the peptide at air/water interface before starting a simulation?

Thanks in advance


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