Re: amber-developers: ene and ener array mess in sander

From: David A. Case <>
Date: Sat, 22 Nov 2008 10:08:08 -0500

On Fri, Nov 21, 2008, Ross Walker wrote:
> Does anyone actually understand how the crazy ene / ener mess in sander
> actually works?

I'd advise checking with Ross -- I think he has spent quite a bit of time
working on this.

There is a set of comments starting at line 1099 of force.f which might be
a start some real code comments.

I believe the use of an offset of 23 goes back to Chandra Singh(!), but it
might be even older (i.e. Paul Weiner).

In the earlier attempt to implement the charmm ff (e.g. Amber9), I just
added the Urey-Bradley energy into the bond term, and the impropers into the
dihedral term, thus avoiding the problem you point out. But that was just a
continuation of the "path of least resistance" approach.

Received on Fri Dec 05 2008 - 16:22:06 PST
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