AMBER Archive (2009)

Subject: Re: [AMBER] Re: AMBER: Re: nmode error: bad nonbon (amber 10)

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Jan 14 2009 - 07:13:18 CST

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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