[MMTK] Minimization

Matias Saavedra matias_saavedra at yahoo.com
Wed Sep 7 00:14:55 CEST 2005


Hi Konrad. i'm trying to perform a minimization with a
small protein (50 residues) in order to go faster...
but each minimization step takes around 6 seconds, and
after one hour and a half of calculation and 1300
steps, i still have a gradient norm of 3.2.

I would like to now the right moment to stop a
minimization to perform a normal modes analysis.

If a small 50 residues protein takes more than 2 hours
to get minimized, a 300 residues protein takes several
days?

How can i minimize the calculation time?

Thanks a lot!

Matías



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