AMBER Archive (2009)

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

From: Jeremy Harris (jphillipharris_at_gmail.com)
Date: Tue Jan 13 2009 - 15:58:36 CST

Thanks, you were right about scee. I now have the nma energies matching
those from sander. I also increased smx (0.5) and emx (1.0), which also
prevented the crash.

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.

Thanks again
Jeremy Harris

On Tue, Jan 6, 2009 at 2:32 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Tue, Jan 06, 2009, Jeremy Harris wrote:
> >
> > I'm trying to do a NMA for a 170 residue long protein,
> > step = 0
> > F = -0.117597E+04 GRDMAX = 0.124782E+03 GNORM =
> 0.182217E+02
>
> As I stated in my earlier email, the large value of GNORM here suggests
> that the energies you are getting in sander are not equal to those in
> nmode. Check the components carefully. The most likely problem is that
> the default value for scee is *not* the same in nmode as it is in
> sander.
>
> ...dac
>
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