help! Non bond list overflow!

From: Zhang Jian <>
Date: Wed 13 Nov 2002 02:56:39 -0800 (PST)

Dear AMBER users,

I run sander in parallel to calculate a protein with
36 residues and about 3000 waters, totally 8864 atoms.

I gave the following command in a SGI IRIX machine,
mpirun -np 8 sander -O -i ...
then got
 * NB pairs 206 317419 exceeds capacity
( 317571) 4
 EWALD BOMB in subroutine ewald_list
 Non bond list overflow!
 check MAXPR in locmem.f
I examined the file locmem.f, ew_direct.f and
ew_setup.f, then know that it is because
num+numpack>maxnblst (206+317419>317571)
in ew_direct.f.
Since maxnblst=MAXPR, I changed the line
BUT numpack also increased by 1000! faint! so the
problem remains same. To increase maxnblst in
ew_setup.f will result in same problem.

Of course I have UGLY method to deal with it, but
could anybody give me a better advice?

Thank you very much!

Best Regards,
Jian Zhang

p.s. this error seems only occur when running sander
in parallel.


Jian Zhang, Dr
Institute for Biophysics
Nanjing University
22 Hankou Road, Nanjing 210093
P. R. China
Tel: 86-25-3594476
Fax: 86-25-3595535

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Received on Wed Nov 13 2002 - 02:56:39 PST
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