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

[David van der Spoel]

OZGE ENGIN wrote:
> 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.

you can find it in the archives on the website.

> 
> Thank you very much
> 
> Ozge
> 
> -----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
> 
> Ozge.
> 
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se