AMBER Archive (2009)

Subject: Re: [AMBER] second derivative matrix calculation

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Feb 06 2009 - 07:19:52 CST


On Fri, Feb 06, 2009, Marie Brut wrote:
>
> Could somebody provide me some informations about the method used to
> calculate the second derivative matrix ?

You pretty much have to follow the source code. Start with nmode, since
it is far simpler, and comes reasonably close to following this book:

%A S.R. Niketic
%A K. Rasmussen
%B The Consistent Force Field: A Documentation
%I Springer-Verlag
%C New York
%D 1977

The code in nab is much more complex, but is also much better commented.
But understanding it is no task for the faint of heart.

...dac

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