Subject: x,y,z vs. internal coordinates

From: [email-masked]
Date: Fri, 17 Jul 1998 14:48:39 +0900

Dear Sir:

        I ask about the following.

(1)  The optimization using x,y,z coordinates is faster than that using
internal coordinates.

(2)  Do you experience that the optimization using x,y,z coordinates
converges  unexpected optimized structure ?   The optimization using
internal coordinates is more safe than the optimization using x,y,z
coordinates ?

        Thank you.

---

From: Richard Gillilan <[email-masked]>
Date: Fri, 17 Jul 1998 08:46:16 -0400

I have heard arguments on both sides. One the one hand,
optimization steps taken in torsion space are thought by
many to follow more closely the natural low energy pathways
in molecules, or at least in proteins. This argument seems to 
be backed up by recent numerical experiments in Ruben Abagyan's group:

Abagyan R.A. and Totrov, M.M. J. Mol. Bio 235 (1994) 983

(which admittedly I have not read), in which they measure how 
far one can move away from a local minimum and still return via
optimization.

Others argue that by restricting the conformational search
to torsion space, the energy barriers are made higher
and the search space becomes "topologically" more complex
as a result. Note that the ECEPP forcefield used by Abagyan
has adjusted torsional barrier heights, supposedly to 
compensate for this.

Personally, I think this is comparing apples with oranges until
someone can perform an optimization in ALL internal coordinates
(including bends, stretches etc. but excluding redundant coordinates)
so that the number of degrees of freedom are the same. I suspect,
however, that internal coords will win for the reasons stated above.
Anybody know of a progam that can do FULL internal coordinate 
optimization?

Richard Gillilan
Cornell Theory Center