AMBER Archive (2004)

Subject: AMBER: water BOX

From: Xioling Chuang (xioling_c_at_hotmail.com)
Date: Mon Jun 07 2004 - 09:09:33 CDT

Dear All,

I am new for amber and I am using amber8. As I have read in amber tutorial
(DNA part) and as I understood, simulation of DNA in rectangular box is not
a proper way, since DNA could rotate (via self diffusion) and will bring the
ends of the DNA near their periodic images and thus, a truncated octahedral
or cubic box is recommended.
However, as I have read from literatures, many researcher used a rectangular
box. Is it a real problem to use the rectangular box, instead of the
recommended one.

Sincerely Yours,
Xioling

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