[gmx-users] corrupted "trr" file?

Hao Hu hao at femto.med.unc.edu
Sun Jan 6 21:41:21 CET 2002


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

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
the size of the trajectory file is about 4G bytes, is this the reason to
all programs to crash?

Thanks very much


Hao Hu

More information about the gromacs.org_gmx-users mailing list