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:
http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions
-Justin
--
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]
<mailto:[email protected]>
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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