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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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