[gmx-developers] (no subject)

Erik Lindahl lindahl at stanford.edu
Sat Jul 12 06:12:18 CEST 2003

Hi Hao,

I guess this is in your modified version, right? Otherwise we should  
look into it.

Segmentation fault means you are reading/writing memory that doesn't  
belong to your process. The most common case is that you allocate an  
array of say length 300 and then try to access element 400.

I guess you are getting a segmentation fault when you access atom 700  
in your print statement. I would recommend spending a couple of hours  
and learn to use a debugger - it's time well invested, and then you can  
stop at any point you want and check the values of variables.

(Said by somebody who still is lazy and uses print statements even  
after learning debuggers - do as I say and not as I do :-)



On Friday, July 11, 2003, at 07:35 PM, 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!
> 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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