Dynamic Movement of Molecule

From: Yuuki Komata <komata_at_complex.eng.hokudai.ac.jp>
Date: Fri 20 Sep 2002 17:03:48 +0900


   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://amber.ch.ic.ac.uk/eqn.txt</a>> here.
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.

Yuuki Komata  komata_at_complex.eng.hokudai.ac.jp
Received on Fri Sep 20 2002 - 01:03:48 PDT
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