Re: AMBER: amber code

From: Andreas Svrcek-Seiler <>
Date: Tue, 24 May 2005 16:18:11 +0200 (CEST)


> I am investigating the sander code especially the subroutine ene.f.
> Does anybody know any good papers or book references on math which
> may help me in understanding the code?
Is your question really about math (and physics)?
There are some books about computational chemistry/physics that might help
you see what's going on inside.
An example (which I found quite ok) is
Andrew R. Leach: "Molecular Modelling: Principles and Applications"
If you look for that book e.g. at, you'll find other books
that might also be quite helpful.
A classic is:
"Computer Simulation of Liquids" by M.P. Allen.

To see what's going on in a technical (computational) sense,
it might be helpful to download NAB
( and have a look
into the sources. They are written in C but much more readable
than "ene.f".
The file to look into is mainly $NABHOME/src/eff.c

You migh also download TINKER
(, which also
contains readable sources (very instructive).

Once done, understanding ene.f and the like will be much easier
(at least according to my experience).

good luck
            ( O O )
               o        Wolfgang Andreas Svrcek-Seiler
               o        (godzilla)
       .oooO            Tel.:01-4277-52733
       (   )   Oooo. 
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Received on Tue May 24 2005 - 15:53:00 PDT
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