Re: E going up and down???

From: David A. Case <>
Date: Wed 14 Aug 2002 15:16:05 -0700

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).


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Wed Aug 14 2002 - 15:16:05 PDT
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