Dear Zhen Chen
Protein is located stranger(sometime at the one side of the protein,in other
frame other side). Its not a problem. Your simulation is fine. it is due to
you had given PBC. thats why. You can reset your trejectory using trjconv.
regards
Ravi Datta Sharma Lecturer, Bioinformatics,
Department of Microbiology,
CCS Unversity,
Meerut
--- On Wed, 3/6/09, sheerychen <[email protected]> wrote:
From: sheerychen <[email protected]>
Subject: [gmx-users] protein running out of box
To: [email protected]
Date: Wednesday, 3 June, 2009, 7:07 PM
Hello, every body. I have running a MD for 10ns. However, after 5ns part of
protein will running out of the box and be located at other part of the water
box. And the whole structure seems ver strange. It seems that it was caused by
the mass translation but I have used the comm_mode=Linear. Any suggestions?
--
Zhen Chen,
Department of Bioprocess and Biosystem Engineering,
Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany
Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: [email protected]
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