AMBER Archive (2009)

Subject: [AMBER] Optimization problem

From: Daniel Emery (
Date: Thu Feb 12 2009 - 04:01:49 CST


I performed a 5ns MD with sander on a system with about 30'000 atoms and
no periodic conditions.
Everything it's fin along the dynamic.
After that I extract, with ptraj, the average structure of the last 50ps
of the MD.
I try to optimize this structure and I give a drms at 0.05. But the RMS
don't converge to this value. I have a minimum value at something like
I tried to just use the conjugate gradient method or just the steepest
descent or a mix of the two but I have always the same problem.

Do you have any idea about a strategy I can adopt to better optimize my
Any suggestions are welcome.

Thanks in advance for your propositions and your help.


EMERY Daniel
Ph.D. Student (Lab. R1)
Department of Organic Chemistry
University of Geneva
30, quai Ernest-Ansermet
CH-1211 Geneva 4
+41 22 379 61 55

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