AMBER Archive (2004)

Subject: Re: AMBER: understanding SANDER source code

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Sun Mar 21 2004 - 13:47:40 CST

Hi,

I am not aware of any flow charts, data flow diagrams, module hierarchies,
etc. One could use tracing to follow the execution of some representative
simulations. A simple tracing module is included in Amber 8.
A debugger could also be used.

However in the big picture one wonders
why you trying to understand sander source code line by line ?
While it is said that programming something, like teaching something,
can lead to a thorough understanding of that thing, it is not necessarily
a productive use of one's time. Certainly reading the literature
should come first.

Sander is really a collection of programs; it has many features,
optimized code sections, and quirks. Tinker is perhaps a better
program to study for pedagogical purposes.

Scott Brozell

On Sat, 20 Mar 2004, myang wrote:

> I am trying to understand sander source code line by line, and find it's
> rather frustrating. Can anyone share his/her experience? Or where can I find
> the basic frame, like a flow chart, for sander. Thanks!
>
> Best & Regards,
> Yang
>
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