AMBER Archive (2005)

Subject: RE: AMBER: non bond over flow

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Dec 29 2005 - 10:15:35 CST

It looks like you are using Amber 7 which has a header file called sizes.h
which defines certain static limits. One of those limits is the maximum
number of pairs in the non-bond list. This has been exceeded during your
simulation causing things to stop. You can get around this by editing
sizes.h in $AMBERHOME/src/sander and increasing the value of maxpr and then
recompiling. However, I suspect that, unless your system is large, there are
other problems with your simulation. The fact that it took 3 to 4 ps to
crash suggests that your density has increased considerably during this
time. An increase in density results in more atoms being within a given cut
off and so more entries in the non-bond list. Similarly a large cut off will
lead to a large number of pairs on the non-bond list. What are you using for
your cutoff value? For PME simulations you should use a cut off of 8
angstroms. More than this makes little, if any, difference.
 
If you are using an 8 angstrom cutoff, and there is nothing obviously wrong
with your simulation, just a steady increase in density to the value you
expect then I would just edit MAXPR in sizes.h and recompile sander.
 
All the best
Ross

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
S.Sundar Raman
Sent: Wednesday, December 28, 2005 19:50
To: amber_at_scripps.edu
Subject: AMBER: non bond over flow

dear amber friends,
i had problem when i did the solvent equilibration for my molecule, it stops
after 3 to 4 ps. it shows the following error.
 
 * NB pairs 186 4999941 exceeds capacity ( 5000000) 0
 SIZE OF NONBOND LIST = 5000000
 EWALD BOMB in subroutine ewald_list
 Non bond list overflow!
 check MAXPR in sizes.h
pls help me how to find the solution for this problem.
thanks in advance 

-- 
S.Sundar Raman
Chemical Lab,
CLRI
Chennai-20
ph: 044-24411830 

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