[gmx-users] trajectory file problem

Luciane Vieira de Mello mello at cenargen.embrapa.br
Fri Jan 24 23:06:01 CET 2003


I already posted a mail reporting that the ngmx visualisation (at least on
our, Linux) machines only read 1.9ns of a 10ns trajectory.  After this
the program froze and had to be killed.  Other Gromacs programs didn;t
seem to have this problem.  Now there's a another issue which I think is

Trying to manipulate these files gives us Linux input/output errors.  What
strikes me is that the errors (when FTPing, copying, splitting - any file
manipulation) occur around 20% into the file.  In other words be can FTP,
for example, 20% of the file before we get an error.  What's important is
that this happens *both* for the xtc and for the trr.  This leads me to
wonder if ngmx, on crashing, has not left some kind of problem in these
files at the 20%/1.9ns mark.  Has anyone else seen this?  What could the
problem be?

We now have the practical issue of trying to recuperate the trajectories.
We can get the first 1.9ps but the rest is tricky.  I've just realised
that I can tail most of the rest of the xtc trajectory (tail
--bytes=1300m traj.xtc >) but when I try to open it I get

Fatal error: Magic Number Error in XTC file (read 313737432, should be

Similarly, I can get the latter part of the trr file.  Then I
get the error

trn version:
Last frame         -1 time    0.000
WARNING: Incomplete header: nr 0 time 0
Fatal error:
Couldn't read time from first frame.

Does anyone have any ideas how to solve the problem of the file, or at
least how to recuperate the maximum possible?

many thanks in advance


|                  Dra. Luciane Vieira de Mello Rigden                    |
| e-mail: mello at cenargen.embrapa.br                                       |
| Embrapa Recursos Geneticos e Biotecnologia                              |
| Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
| PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
| 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |

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