AMBER Archive (2006)

Subject: Re: AMBER: non bond list overflow

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Tue Feb 07 2006 - 10:32:18 CST

Thank you for your reply--that was exactly the mistake that I was making.
But now that I'm looking at sizes.h in /src/sander, I'm not sure what to do.
Do I just increase MAXPR, and if so, how high can I increase it without
causing problems? I am hesitant to change source code without knowing
exactly what I'm doing.

Thank you very much for your help.

Kenley

On 2/7/06, David A. Case <case_at_scripps.edu> wrote:
>
> On Mon, Feb 06, 2006, Kenley Barrett wrote:
> >
> > I recently tried to run a minimization of a large system (about 12000
> heavy
> > atoms in the solute and then about 30000 water molecules). The
> minimization
> > stopped with the following error:
> >
> > * NB pairs 191 17999833 exceeds capacity ( 18000000) 0
> > SIZE OF NONBOND LIST = 18000000
> > EWALD BOMB in subroutine ewald_list
> > Non bond list overflow!
> > check MAXPR in sizes.h
> >
> > I looked for the sizes.h file in $AMBERHOME/src/sander and couldn't find
> it.
>
> I guess we need to know what version of Amber you have or are running.
> Amber 7 is the last version that had the error message "check MAXPR in
> sizes.h", and it *does* have a sizes.h file in amber7/src/sander.
>
> Amber 8 does not have either the error message, nor the sizes.h file.
>
> Is it possible that you are running an executable verison of amber7, but
> that
> $AMBERHOME points to the source code for Amber 8? Other than that, I
> can't
> really think how the situation you describe could happen. [Doesn't mean
> that
> it can't/didn't happen some other way...it may just be my lack of
> imagnation.]
> If this doesn't help, let us know which version you are using.
>
> ...regards...dac
>
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