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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Received on Wed Nov 03 2004 - 06:53:00 PST
