AMBER Archive (2005)

Subject: Re: AMBER: Sander and NMODE energy minimization

From: David A. Case (case_at_scripps.edu)
Date: Sun Jan 02 2005 - 16:47:28 CST

On Sat, Jan 01, 2005, fangyu liang wrote:
>
> 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?

Defaults for variables are given in the Users' Manual.

>
> 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?

Newton-Raphson can only be used for small systems; it is generally
too expensive for large molecules.

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

I hesitate to answer: you will benefit by learning how to answer such
questions yourself. But look at src/sander/runmin.f and src/nmode/nrch.f

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

yes.

..dac
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