AMBER Archive (2008)

Subject: AMBER: Sander crashes >99999 atoms

From: plmallip_at_mail.uh.edu
Date: Thu Jun 12 2008 - 18:26:57 CDT

Dear colleagues,
 
My system has 1060 residues (8730 atoms). The size of the system increased to >99999 atoms, when I added 10 A water. I am using amber 8 on a linux cluster amd64. When, I try to minimize, using 4 CPUs - I get the following error.
 
forrtl: severe (174): SIGSEGV, segmentation fault occurred.

My test run, with a smaller system was successful.
 
My mdin file is :
 
Minimization with restraints on solute
&cntrl
 imin=1, maxcyc=200,
 ntpr=5,
 ntr=1,
&end
restrained atoms
100.0
RES 1 1060
END
END
 
I request your suggestion in this regard.
 
thanks and regards,
Prema.

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