On Wed, Aug 14, 2002, Jiyoung Heo wrote:
>
> Is it possible that the total energy is going up and down during
> minimization?
Yes, this is to be expected. At individual steps, the minimizer may try
a conformation that has a higher energy than the current configuration.
That's (roughly) how it figures out which direction to go, i.e by getting
a sense of which directions to avoid.
There are many good disucssions of steepest descent and conjugate gradient
algorithms in the numerical analysis literature (and in the chemical
modelling literature as well).
..dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Aug 14 2002 - 15:16:05 PDT
