AMBER Archive (2002)

Subject: Re: Minimization in GB-SA-E-Spikes, LINMIN

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 17 2002 - 19:43:57 CDT


On Tue, Jul 16, 2002, Sarangan Ravichandran wrote:
>
> During minimization,
> I keep seeing energy spikes at regular
> intervals

The conjugate gradient routine does not go downhill at every step; it
periodically tries new directions, and sometimes makes too big a move (leading
to a very high energy). It then recognizes this, and returns to low energy
reasons.

To study this in any detail, you would need to set ntpr to 1 (and probably
modify the code to output more information about what part of the minimizer
was operative at each step.) Incorporating a better minimizer has long been
a goal, but not one we have made much progress on.....

For now, what you describe is expected behavior, as far as I can tell
from the information you provided.

..hope this helps....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 ==================================================================