[gmx-developers] (no subject)

[David]

On Sat, 2003-07-12 at 04:35, Fan Hao wrote:
> Hi, All:
> 	I meet a problem which cause "segmentation fault, core dump",
> when I did mdrun. I used grompp -norenum ... to produce my topol.tpr
> and it was ok. Later I need to use all the coordinates of the molecule
> atoms in force(). The molecule has 833 atoms while I only can got 
> around 700 atom's coordinates by output rvec x[] using
> for(i=0;i<833;i++)
>    fprintf(stdlog,"%f %f %f\n",x[i][0],x[i][1],x[i][2]);
> I am not sure which mistake I have made. Any hints will be sincerely
> appreciated. Thanks a lot in advance!

Apart from using a debugger, you could start with running mdrun -debug
which will give you a lot of extra output.
Rather than writing such print statements you could use some of the
library functions:
  if (debug)
    pr_rvecs(debug,0,"my coordinates",x,natoms);

Don't put numbers (like 833) in the code if you can avoid it!


> 
> Best regards
> 
> Yours sincerely
> 
> Hao Fan :-)
> 
> -------------------------------------------------------------------------
> Drs. Hao Fan                            email F.Hao at chem.rug.nl
> Lab. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4                            9747 AG GRONINGEN
> The Netherlands
> -------------------------------------------------------------------------
> 
> 
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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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