AMBER Archive (2004)

Subject: Re: AMBER: Amber: BOMB

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 08 2004 - 09:55:04 CDT

On Wed, Sep 08, 2004, Helios wrote:

> Dear all, I am minimizing a protein with ~15984 atoms (included water
> molecules) on SGI system (CPU:1*350MHz, Main Memory:256Mb, Swap:128Mb).
> When running with sander, after five
> seconds or so, the calculation always crashes, and the output is this:
>
> * NB pairs 15525 7199515 exceeds capacity ( 7200000)
> SIZE OF NONBOND LIST = 7200000
> EWALD BOMB in subroutine ewald_list
> Non bond list overflow!
> check MAXPR in sizes.h
>
> I have increased the value for MAXPR already, and it can't seem more than
> 7200000. Does this question could be solve if I buy more memory (e.g.,
> 512MB) or any parameters I need to correct?

We are going to need more information: which version of Amber? is this a
periodic or non-periodic simulation? what is your cutoff?

Look at the Run.dhfr.min test case (in $AMBERHOME/test/dhfr). This minimizes
a larger system, and presumably works on your system. Try to find the
differences between your example and this one.

...good luck...dac

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