AMBER Archive (2009)

Subject: [AMBER] Optimization problem

From: Daniel Emery (Daniel.Emery_at_unige.ch)
Date: Thu Feb 12 2009 - 04:01:49 CST

Hi,

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
0.2...
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
structure.
Any suggestions are welcome.

Thanks in advance for your propositions and your help.

Regards,
Daniel 

-- 
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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