Re: [AMBER-Developers] lmod xmin problems with sander and sqm

From: <istvan.kolossvary.hu>
Date: Fri, 11 Dec 2009 03:54:26 +0100

Andreas,

> Yes, it is normal that the number of optimization steps strongly depends
> on the system under investigation. The accuracy of the final
> optimization results of sqm has been established (see below), so it is
> only about efficiency. I compared three programs given identical
> starting conditions with optimizations in the same coordinate space. It
> is just the optimization algorithms that differ. Here is some updated
> data for NMA (I started from a reasonably distorted structure) which
> includes mopac2009 with L-BFGS (all AM1 data):
>
> GRMS steps program algorithm E(final)
>
> 0.02 47 orca2.6.35 BFGS -1008.31272
> 0.02 90 mopac2009 EF -1008.31236
> 0.02 169 mopac2009 L-BFGS -1008.31236
> 0.02 186 sqm L-BFGS -1008.31227
>
> 0.05 47 orca2.6.35 BFGS -1008.31272
> 0.05 87 mopac2009 EF -1008.31236
> 0.05 109 mopac2009 L-BFGS -1008.31168
> 0.05 125 sqm L-BFGS -1008.31172
>
> GRMS in kcal/(mol*A)
> E(final) in eV (electronic energy)
> EF = Eigenvector following

XMIN has an L-BFGS preconditioned TNCG option, which requires
significantly less steps than L-BFGS and is also capable of lowering
the gradient to much smaller RMS. We reset sqm to use this method with
Dave, but he said he would make it an option in the test program.

    Istvan



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Received on Thu Dec 10 2009 - 19:00:02 PST
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