AMBER: Minimized structure

From: Yam <>
Date: Wed, 27 Jul 2005 20:02:03 -0700 (PDT)

Dear all,

Hello. The following questions are related to
minimizations, and any form of replies will be most
welcome. Thanks in advance.

1. How can we be assure that our structure is
resonable after minimizations, besides looking into
starting and ending energy and RMSD?

2. What does GMAX means in the minimization output

3. Does SHAKE really affects the bondings involving H
in minimizations?

4. Is it ok if we use leap as a checking tool for any
errors in structure after minimizations?

5. Any exception if we are running minimizations or MD
on very huge structure (like 100K atoms)??

Thanks a lot.

Best Regards,

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Received on Thu Jul 28 2005 - 04:53:01 PDT
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