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:
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4. RESULTS
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APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
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
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* 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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Received on Tue Feb 07 2006 - 06:10:09 PST
