[gmx-users] protein running out of box

ravi sharma rdsharma_4u at yahoo.com
Wed Jun 3 16:07:57 CEST 2009

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.


Ravi Datta Sharma  Lecturer,  Bioinformatics,
Department of Microbiology,
CCS Unversity,

--- On Wed, 3/6/09, sheerychen <sheerychen at gmail.com> wrote:

From: sheerychen <sheerychen at gmail.com>
Subject: [gmx-users] protein running out of box
To: gmx-users at gromacs.org
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: zhen.chen at tuhh.de

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