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.
AMBER mailing list