AMBER Archive (2006)

Subject: AMBER: non bond list overflow

From: Kenley Barrett (
Date: Mon Feb 06 2006 - 21:43:06 CST

Dear Amber Users,

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:


 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.3242E-14 at 2.436720
| CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960

 * 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 did find a file called sizes.h in the $AMBERHOME/src/anal, but it doesn't
contain a variable called "MAXPR". I would be very grateful for any advice
that anyone can offer. If the problem is the size of my system, I would
appreciate any feedback on the size of system that AMBER is capable of
handling, and how I can arrange things to help AMBER work with a big system.

Thank you very much for your help.

Kenley Barrett

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