Hi,
I got .out file, the last lines are:
NSTEP ENERGY RMS GMAX NAME NUMBER
70 -2.8473E+04 2.9235E+02 1.1773E+05 SG 5704
BOND = 213801.9515 ANGLE = 7045.5244 DIHED = 9929.7416
VDWAALS = 61906.9355 EEL = -375745.2216 HBOND = 0.0000
1-4 VDW = 7253.1165 1-4 EEL = 47335.0552 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
75 1.3756E+11 1.2563E+10 3.7524E+12 SG 16034
BOND = 90981.4516 ANGLE = 8650.2958 DIHED = 10103.7688
VDWAALS = ************* EEL = -388139.7525 HBOND = 0.0000
1-4 VDW = 26843.2678 1-4 EEL = 47112.3776 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
80 1.3716E+11 1.2523E+10 3.7405E+12 SG 16034
BOND = 90981.4963 ANGLE = 8650.2956 DIHED = 10103.7688
VDWAALS = ************* EEL = -388139.7508 HBOND = 0.0000
1-4 VDW = 26843.2678 1-4 EEL = 47112.3775 RESTRAINT = 0.0000
mdinfo file has:
NSTEP ENERGY RMS GMAX NAME NUMBER
80 1.3716E+11 1.2523E+10 3.7405E+12 SG 16034
BOND = 90981.4963 ANGLE = 8650.2956 DIHED = 10103.7688
VDWAALS = ************* EEL = -388139.7508 HBOND = 0.0000
1-4 VDW = 26843.2678 1-4 EEL = 47112.3775 RESTRAINT = 0.0000
My system has 17258 atoms including H's. I would like to mention that I am new to using this software. So, when sander worked for small system, I thought, its because of more number of atoms. I was able to minimize solvent succesfully, by constraining protein. So, the problem seems to be related to system memory? I am not sure.
Thanks & regards,
Prema.
----- Original Message -----
From: "David A. Case" <case.scripps.edu>
Date: Thursday, June 12, 2008 8:29 pm
Subject: Re: AMBER: Sander crashes >99999 atoms
To: amber.scripps.edu
> On Thu, Jun 12, 2008, plmallip.mail.uh.edu wrote:
>
> > 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.
>
> I doubt that this has anything directly to do with the number of
> atoms. We
> run systems with more than 100000 atoms a lot.
>
> Did you get any output? Does the segmentation fault occur
> immediately (i.e.
> before the first energy step) or later? Does the job
> work in serial mode?
>
> There is something odd about your system: a protein with 1000
> residues would
> ordinarily have about 16,000 atoms (not including the
> solvent). Is there
> something unusual in your sequence that it has so few atoms?
>
> Unfortunately, a segfault is not a very informative error
> message. But
> usually some detective work can narrow down the
> possible/probably causes of
> such a failure.
>
> ...dac
>
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Received on Sun Jun 15 2008 - 06:07:44 PDT
