AMBER Archive (2002)

Subject: Dynamic Movement of Molecule

From: Yuuki Komata (komata_at_complex.eng.hokudai.ac.jp)
Date: Fri Sep 20 2002 - 03:03:48 CDT

Hello,

   I am simulating DNA binding protein on Amber6. This protein moves
its pair of arms very dynamically, and seems to hold DNA.

   Question is about the equation<a href=http://www.amber.ucsf.edu/amber/eqn.txt> here</a>.
Is the first part of V uses some approximation? If so, dynamic movement
of my protein would be nonsense?
   I read r0 means 'avarage of bond length', but what average? Is it
calculated on every MD or already difined?

   I am not familiar with such problems... Suggestions needed to help my
MD from nonsense!

   Thank you very much. 

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Yuuki Komata  komata_at_complex.eng.hokudai.ac.jp