On Tue, Jan 13, 2009, Jeremy Harris wrote:
>
> I'm just curious now about the time it takes for minimization. It is taking
> about 15 min per minimization step, is this normal? The protein has 150
> residues.
That sounds about right for Newton Raphson. You might want to use the
xmin minimizer to get to a low RMS gradient (below 10**-5) before
starting NR. Also, bear in mind that nmode is very old code, and that
NAB allows you to do normal modes with GB (rather than just vacuum), and
in a code environment that is still being maintained.
...dac
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Received on Fri Jan 16 2009 - 01:09:22 PST
