AMBER Archive (2009)

Subject: Re: [AMBER] Optimization problem

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Feb 12 2009 - 06:58:17 CST

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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