AMBER Archive (2004)

Subject: AMBER: Amber: BOMB

From: Helios (p9890101_at_mail.ncku.edu.tw)
Date: Wed Sep 08 2004 - 07:18:11 CDT

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?

p.s. When I use "unlimit datasize" command, it happens "Unlimit: datasize: Can't remove limit".

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