AMBER Archive (2002)

Subject: Re: problem in sander

From: David A. Case (case_at_scripps.edu)
Date: Fri Oct 11 2002 - 10:00:53 CDT

On Thu, Oct 10, 2002, Ioana Cozmuta wrote:
>
> I am trying to do a minimization for a protein (total number of
> residues 2051 plus 818 crystallografic waters...

keep in mind that you are looking at a system that is much larger (by an
order of magnitude) than proteins that Amber is more typically used for.
The mailing list will look at problems, but you should expect to have to
work out lots of problems for yourself, and to learn how the code works.
I encourage you also to think hard about what you plan to learn about this
system (given that you won't be able to do much sampling), and whether some
smaller piece of it might not serve your purposes equally well.

> Failed to allocate memory for ipairs: 604076661
>
> What is the best thing to do in this case?

You will need to find a machine with at least 600 MBytes of physical (or
virtural) memory.

> Increase lastist in the &cntrl namelist

Add a "lastist=<number>," to your &cntrl namelist, and re-run. You may have
to experiment to see what value you need, but it will need to be larger
than the default one.

>
> I am running this job on 4 processors however only one seems to be
> failing. Any idea what is causing this?

The master node is noting that there is not enough memory for the job, and it
is stopping the whole run.

>
> About the lastist: In sizes.h it is advised to override the MAX_ISTACK
> value by defining indeed lastist in the &cntrl list. What is the limiting
> value that one can use for lastist?

Limited by available memeroy.

..dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================