AMBER Archive (2009)

Subject: Re: [AMBER] nab conjgrad min problem

From: Jeremy Harris (jphillipharris_at_gmail.com)
Date: Mon Jan 19 2009 - 09:00:30 CST

Oh, that was silly - x was too small. x[ 10000 ] works well. I believe I
have nab working, so thank you

Jeremy Harris

On Fri, Jan 16, 2009 at 3:33 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Fri, Jan 16, 2009, Jeremy Harris wrote:
>
> > Thanks for the previous help - you recommended the NMA from nab over
> nmode.
> > I've been fiddling around with nab, and can't seem to get it to do a
> simple
> > conjgrad minimization. On the first step it will give an enormously large
> > negative energy, and then change the position of one of the atoms by an
> ^^^^^^^^ positive?
>
> > equally large number. Could you also explain the fourth argument in
> > mme_init?
> >
> > my min.nab file and output are:
> >
> > molecule p;
> > float x[ 4000 ], fret, dummy[2];
>
> Are you sure that 4000 is big enough? It needs to be at least 3 *
> natom.
>
> It's possible there is a bug in the R94 code path -- try a short
> minimization with dielc=C (or R) to see if you get the same behavior.
>
> The fourth argument to mme_init() gives an array of reference
> coordinates, which are used to keep atom positions close to the
> positions they have in the reference array. Only relevant if you set
> wcons > 0.
>
> ...dac
>
>
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