AMBER Archive (2004)

Subject: RE: AMBER: Changing MAXPR in Amber 8?

From: Robyn Ayscue (kajsicat_at_yahoo.com)
Date: Fri Jun 18 2004 - 15:03:06 CDT

Ross,

Thanks for your help! We are, in fact, using a 32-bit
machine, and when we changed the cutoff from 9.0 to
8.0 in the input file the dynamics ran beautifully.
Again, thanks!

Yours,
Robyn Ayscue

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Dear Robyn,
>
> In sander v8.0 memory allocation is now done
> dynamically instead of
> statically and so the setting of values such as
> MAXPR in sizes.h is now no
> longer necessary.
>
> I suspect that the error you are getting could be
> related to the use of a
> cut off. If your cut off is too large, and your
> system is big, then the
> number of pairs that need to be calculated will
> exceed what can be stored in
> a 32bit integer (2.147x10^9). Are you running on a
> 32 bit machine? How big
> is your system? And what value are you using for the
> cut off?
>
> Also can you post your input and output files so
> that we can see what the
> error may be.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:-
> ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available
> on request |
>
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Robyn Ayscue
> > Sent: 18 June 2004 12:08
> > To: amber_at_scripps.edu
> > Subject: AMBER: Changing MAXPR in Amber 8?
> >
> > All,
> >
> > Hi! I'm using Sander in Amber 8, and I want to
> > increase the MAXPR in the sizes.h file to correct
> an
> > EWALD BOMB error I've been getting with one of my
> > molecular dynamics runs. However, when I cat the
> > sizes.h file, there is no MAXPR tag mentioned
> there.
> > Does anyone know of any idea to remedy this?
> Thanks
> > for your time!
> >
> > Yours,
> > Robyn Ayscue
> >
> >
> >
> > __________________________________
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