[gmx-users] g_density problem segmentation fault glibc detected

[maria goranovic]

Here are the answers to the questions:

Did see the trajectory. Looks fine

Did start from different initial time frames, and thicker slabs, problem
does not go away

Yes, the simulation has run for ~ 80 ns. It is equilibrated

Which log file ? What I reported was from the log file


On Tue, Jun 10, 2008 at 3:30 PM, Peyman Yamin <
Peyman.Yamin at cbi.uni-erlangen.de> wrote:

> Have you seen the trajectory? Did you try to start from different frames?
> Is
> your system equilibrated?
> check log file!
>
> Peyman
>
>
> On Tuesday 10 June 2008 13:35, himanshu khandelia wrote:
> > Hi,
> >
> > I am trying to calculate the density in a bilayer simulation:
> >
> > echo 27 | g_density -f lipiddrg.xtc -n all.ndx -s all.tpr -o head.xvg
> > -sl 200 -b 40000
> >
> > The system size is about 6.5 x 6.5 x 9.6
> >
> > I get the following error, after g_density has read most of the
> trajectory:
> >
> > *** glibc detected *** g_density: free(): invalid next size (fast):
> > 0x0000000000877e70 ***
> >
> > Can anyone please point out what the problem might be?  The same
> > command works for other trajectories for me.
> >
> > Thank you
> >
> > -Himanshu
> > MEMPHYS, SDU, Denmark.
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> --
> Peyman Yamin
> Lehrstuhl fuer Thermische Verfahrenstechnik
> Universitaet Erlangen-Nuernberg
> Egerlandstr. 3
> 91058 Erlangen
> Phone: +49(0) - 9131 - 85 27671
> Mailto: peyman.yamin at cbi.uni-erlangen.de
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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