[gmx-users] protein running out of box

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 3 15:46:08 CEST 2009

sheerychen wrote:
> 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?

What you are seeing is a normal consequence of periodicity.  There is no "side" 
in an infinite system:



> -- 
> 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 
> <mailto:zhen.chen at tuhh.de>
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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