AMBER Archive (2004)

Subject: AMBER: SANDER BOMB in subroutine nonbond_list

From: Marc Perea (marc.perea_at_uab.es)
Date: Tue Nov 02 2004 - 06:45:34 CST

Dear AMBER Users,

I have a problem running sander in the following scenario :

Machine : Pentium IV 3.0 Ghz & Linux 2.4
Compiler : Portland Group pgf90 + Mpich 1.2.5.2
Sander input :

minimization of the solvent
 &cntrl
     imin=1,
 
     ntpr=100, ntr=1, restraint_wt=100.0,
     restraintmask=':1-30',
 
      ntf=1, ntb=1, dielc=1., cut=10.,
      scnb=2., scee=1.2, ntc=1,
 
     ntp=0, pres0=1., comp=44.6, taup=0.2, npscal=1,
 
     maxcyc=500, ncyc=200,
 
 &end

I run this and it doesn't calculate anything, the following error
appears on the pro.sanderout file :

-----------------------------------------------------------------------
--------- 4. RESULTS
-----------------------------------------------------------------------
---------
 ---------------------------------------------------
 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 = 0.2763E-14 at 2.626100
| CHECK d/dx switch(x): max rel err = 0.7525E-11 at 2.750640
 ---------------------------------------------------
 
 * NB pairs 1644 21012371 exceeds capacity ( 21013056) 0
     SIZE OF NONBOND LIST = 21013056
 SANDER BOMB in subroutine nonbond_list
 Non bond list overflow!
 check MAXPR in locmem.f

Does anybody know how can I start tracking down the problem ? I tried
with a non-parallel version, also with a patched version of amber
(http://amber.scripps.edu/bugfixes/8.0/bugfix.all) but still no luck.

Thanks in advance, Best Regards,
Marc 

-- 
Marc Perea - Systems Administrator
Computational Medicine Laboratory, Bioestatistics Dept.
Universitat Autonoma de Barcelona, http://lmc.uab.es
Tel : (+34) 93 581 38 12
Fax : (+34) 93 581 23 44
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