AMBER Archive (2009)

Subject: Re: [AMBER] Optimization problem

From: Daniel Emery (
Date: Thu Feb 12 2009 - 08:11:14 CST

I actually have run this optimization for 150'000 steps and I have no
explicit waters in my system...

Thanks for your proposition for using xmin but I have a problem when I
try to run the following input file with AMBER 9:

imin=1, maxcyc=150000, ntmin=3,
drms=0.05, ntb=0,
cut=12.0, ntpr=100,

In the output file, I have an error message:

  LMOD XMIN Minimization.
 ERROR: LMOD XMIN is unavailable.

Do you know is wrong with that??

Thanks once more


David A. Case wrote:
> On Thu, Feb 12, 2009, Daniel Emery wrote:
>> 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...
> You don't say how many minimization steps you used, or whether or not
> you have explicit waters. It can take many tens of thousands of steps
> to minimize to a low rms for 30,000 atoms. The xmin minimizer will
> generally do a better job than conjugate gradients, so you might try
> that.
> ...dac
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> AMBER mailing list

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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