AMBER Archive (2009)

Subject: Re: [AMBER] Extreme optimization problems

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Aug 06 2009 - 10:51:23 CDT

On Thu, Aug 06, 2009, ondrej.prenosil_at_marge.uochb.cas.cz wrote:
>
> we have a really strange and mad goal - to optimize protein (4881 atoms)
> so the GMAX is less or equal to 1e-7. Is there somewhere a good and
> experienced soul, that can help?

We do this routinely, using the xmin minimizer in NAB or sander. With
Newton-Raphson minimization, you can easily get below 10*-11. Such a
simulation makes good sense in implicit solvent (like GB); it might not work
so well with explicit solvent and periodic boundaries.

Look at amber10/test/nab/txmin.nab. Increase maxiter and
decrease the grms_tol value, and things will probably work.

...good luck....dac

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