[gmx-users] floating point exception

[David]

On Fri, 2003-06-27 at 20:54, Mr.Sridhar wrote:
> Hello gmx users
> 
> In one of my MD run jobs the job terminated with an error saying,
>              "Floating exception - core dumped".
> I was running MD simulations for a protien and the same protein with a
> point mutation in it. MD ran well for Wildtype but for mutant type even at
> the stage of Energy Minimization its giving this error. The log message is
> ##########################################################################
>                      Gnomes, ROck Monsters And Chili Sauce
> 
>                             :-)  VERSION 3.1.4  (-:
> 
> 
>        Copyright (c) 1991-2002, University of Groningen, The Netherlands
>          This program is free software; you can redistribute it and/or
>           modify it under the terms of the GNU General Public License
>          as published by the Free Software Foundation; either version 2
>              of the License, or (at your option) any later version.
> 
>                               :-)  cron_squid  (-:
> 
> Option     Filename  Type          Description
> ------------------------------------------------------------
>   -s b4em_WT_N453S.tpr  Input         Generic run input: tpr tpb tpa
>   -o em_WT_N453S.trr  Output        Full precision trajectory: trr trj
>   -x       traj.xtc  Output, Opt.  Compressed trajectory (portable xdr
> format)
>   -c em_WT_N453S.gro  Output        Generic structure: gro g96 pdb
>   -e em_WT_N453S.edr  Output        Generic energy: edr ene
>   -g em_WT_N453S.log  Output        Log file
> -dgdl      dgdl.xvg  Output, Opt.  xvgr/xmgr file
> -table    table.xvg  Input, Opt.   xvgr/xmgr file
> -rerun    rerun.xtc  Input, Opt.   Generic trajectory: xtc trr trj gro g96
> pdb
>  -ei        sam.edi  Input, Opt.   ED sampling input
>  -eo        sam.edo  Output, Opt.  ED sampling output
>   -j       wham.gct  Input, Opt.   General coupling stuff
>  -jo        bam.gct  Input, Opt.   General coupling stuff
> -ffout      gct.xvg  Output, Opt.  xvgr/xmgr file
> -devout   deviatie.xvg  Output, Opt.  xvgr/xmgr file
> -runav  runaver.xvg  Output, Opt.  xvgr/xmgr file
>  -pi       pull.ppa  Input, Opt.   Pull parameters
>  -po    pullout.ppa  Output, Opt.  Pull parameters
>  -pd       pull.pdo  Output, Opt.  Pull data output
>  -pn       pull.ndx  Input, Opt.   Index file
> -mtx         nm.mtx  Output, Opt.  Hessian matrix
> 
>       Option   Type  Value  Description
> ------------------------------------------------------
>       -[no]h   bool     no  Print help info and quit
>       -[no]X   bool     no  Use dialog box GUI to edit command line
> options
>        -nice    int     19  Set the nicelevel
>      -deffnm string         Set the default filename for all file options
>          -np    int      1  Number of nodes, must be the same as used for
>                             grompp
>       -[no]v   bool     no  Be loud and noisy
> -[no]compact   bool    yes  Write a compact log file
>   -[no]multi   bool     no  Do multiple simulations in parallel (only with
> -np
>                             > 1)
>    -[no]glas   bool     no  Do glass simulation with special long range
>                             corrections
>  -[no]ionize   bool     no  Do a simulation including the effect of an
> X-Ray
>                             bombardment on your system
> 
> Reading file b4em_WT_N453S.tpr, VERSION 3.1.4 (single precision)
> Reading file b4em_WT_N453S.tpr, VERSION 3.1.4 (single precision)
> Steepest Descents:
>    Tolerance         =  1.00000e+03
>    Number of steps   =         4000
> batch3.sh: 286118 Floating exception - core dumped
> ##############################################################################
> All the conditions of Energy minimization and MD are same for both the
> proteins.
> I don't understand the problem. Is it problem with hardware ?
> Any suggessions to rectify this problem ?

Is it just the structure? i.e. having two atoms on top of each other?
Check your mutation using a graphics viewer.

Otherwise, is this an OSF machine?

> 
> Thank you.
> 
> sridhar
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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