[gmx-users] glibc error with g_density (only for some cases)

Arun kumar arun.target at gmail.com
Fri May 18 10:37:53 CEST 2007

Hai Mark..
              Thanks for your suggestions. I will think about my
problem clearly and will post a message with much care so that every
one can easily read. Also I can get a response.

               About g_density I will check once again the log file
and post the reply here. But I think there is nothing went wrong in my
simulations in between 500 and 1500 time steps. I am able to evaluate
all properties for those frames also. Anyway I will check once again.

Thanks and regards
Arun Kumar

On 5/18/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Arun kumar wrote:
> > Dear gmx-users,
> >                        I want to discuss and understand about an
> > error I am getting only at times.... I am simulating a DPPC double
> > bilayer phase(got the coordinates from Dr Tieleman's website). I used
> > genbox  -cs to get double bilayer. Then i started simulations
> > normally.
> >
> > When I use   g_density -b 500  I get the following error
> >
> > *** glibc detected *** free(): invalid next size (normal):
> > 0x0000000000713260 *** Aborted
> >
> > It is giving a empty density.xvg file
> >
> > I get same error if I use g_density -b 1000
> > I checked the reproducibility of the error...... I am getting it
> > always(I mean I am using g_density once again again,,,,, Not
> > simulating the system once again again)
> >
> > But when I use g_density -b 1500 or more I am getting densities
> > normally.....
> > Actually  i am doing simulations at 4 different temperatures..... But
> > I am getting the error only for three temperatures.... For one
> > temperature Every thing is fine......
> > Gromacs version I am using is : 3.3.1
> > I checked the archives and in google.... I found a similar error in
> > archives for make_ndx
> >
> > After checking in google I came to know that its a common bug with
> > glibc package of different versions.....  Now i want to know is there
> > anything wrong in my simulations(possibilities) and also how I can rid
> > of these errors.........
> You stand a much better chance of getting a response if you make your
> requests easy to read. That means using conventional English
> punctuation, ie. not ending most sentences with an ellipsis. Your use of
> ellipses in the above text makes it read like it is a stream of
> consciousness that you haven't thought through clearly. That makes
> people not want to do your work - thinking clearly about your problem
> and describing it well - and thus never getting around to giving you any
> insight.
> I have never used g_density, but I had look at the man page for 30
> seconds and I can think of two reasons why doing an analysis starting at
> point c would work when it doesn't work starting at a or b, when a<b<c.
> Since it only happens for one of your 4 near-identical simulations, this
> suggests one of my reasons isn't right... and so I think there is a
> problem with your output between b and c for the one that breaks. Go and
> look at the log file and see what went wrong.
> I didn't apply much knowledge here, I just thought about the problem
> clearly. Perhaps this would have occurred to you if you'd thought about
> things this way before posting :-)
> Mark
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Arun kumar.V
M.E Chemical

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