AMBER Archive (2005)

Subject: AMBER: Sander and NMODE energy minimization

From: fangyu liang (fliang_at_usc.edu)
Date: Sat Jan 01 2005 - 23:53:49 CST

Hi,

Please help me for the following four questions:

1)If ntmin(Method of Minimisation) is not specified in the Sander command, what is the default value used by the Amber 8 program? Is it ntmin=0?

2)If Sander can do energy minimization, why is there 'NMODE' program also for energy minimization(with Newton Raphson method)? Is one better than the other? or what is the reason to have both energy methods in Amber 8?

3)What are the actural Amber 8 code files for both Sander and NMODE energy minimization modules?

4)Can I modify those files mentioned in question #3 if they exist?

Thank you very much!

Sincerely,.

Fangyu

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