AMBER Archive (2005)

Subject: AMBER: Minimized structure

From: Yam (yamwaikeat_at_yahoo.com)
Date: Wed Jul 27 2005 - 22:02:03 CDT

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
files?

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,
Yam

                
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