[gmx-users] corrupted "trr" file?

Mehmet Suezen suzen at theochem.tu-muenchen.de
Mon Jan 7 08:58:00 CET 2002


Which linux kernel are you running? As far as I know Linux Kernel 2.2.x
could not handle files >2Gb. May be it is the case, If so It'd be a
solution to
make simulation in smaller pieces. 


Hao Hu wrote:
> Hi,
> I'm a new user of GROMACS. Recently I downloaded the program
> (version 3.0.5) and installed a double-precision version on one Alpha-
> linux machine. Then I created files for a small protein (70 residues)
> solvated in 6771 SPC water molecules. The total number of atoms is
> 21441.
> After energy minimization and a short restrained MD simulation,
> then I started a 3.6 ns simulation. I set the trajectory to be recorded
> every 180 steps (.36ps) . During the begining several days of the
> simulation, I can use "ngmx_d" and "g_rms_d" and "trjconv_d" to
> view and analyze the results although it was not finished. But after
> one certain time point, I can no longer use any of those programs to
> analyze the results. All programs crashed for "Segmentation fault"
> and dumped a core file. If I try to load the program and the core file
> within "gdb", it printed out error information as:
> #0  0x200013dbfd8 in xdr_string (xdrs=0x1202ac990, cpp=0x11fff29a0,
>     maxsize=4270493208) at xdr.c:716
> 716 xdr.c: No such file or directory.
> But I can't find any file named as "xdr.c" in the source. I realized
> that
> the size of the trajectory file is about 4G bytes, is this the reason to
> cause
> all programs to crash?
> Thanks very much
> Sincerely
> Hao Hu
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