Thanks! Removing the box solved the problem. :-)
On Tue, Nov 5, 2013 at 1:34 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Nov 05, 2013, maghtar wrote:
>
> > I have a molecule consist of 81 atoms in vacume and I want to calculate
> the
> > normal modes of it. The first conjgrad minimization is done successfully
> > but in Newton-Raphson after the first step the energy goes to infinity.
> > Does Anyone have any idea what the problem can be? Following you can see
> > the input and output.
> >
> > nblist_box, number of atoms= 81
>
> You say that your molecule is in vacuum, but it looks like the prmtop file
> has box information, and nab is trying to use it. However, normal modes
> (or Newton Raphson, which also uses second derivatives) in nab do not
> support periodic boundary conditions (and, in fact, the periodic support
> in nab is rather limited).
>
> I will add a test to make sure that the code gives a error message if you
> request second derivatives for a periodic system. But for now, you need to
> build a non-periodic system.
>
> Also, you may need to to get a gradient lower than 0.005 before starting
> Newton-Raphson.
>
> Finally, I almost never use Newton Raphson any more (although it should be
> fine for such a small system). The xmin minimizer will generally get you
> to
> an acceptable minimum faster.
>
> ...good luck...dac
>
>
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Received on Tue Nov 05 2013 - 06:30:02 PST
