On 15/07/2011 7:31 PM, Martin Kamp Jensen wrote:
Hello,
I am trying to evaluate energy values of several conformations using a
(pseudo)trajectory. Currently, I am concatenating GROMOS-96 files
(.g96) and using that as a trajectory. For some reason the second
conformation in a trajectory is ignored. So e.g. if I have three
conformations (1.g96, 2.g96, and 3.g96), then concatenate them into
1+2+3.g96, and then use the latter file as a trajectory, the
conformation of 2.g96 is ignored when using mdrun -rerun with a
suitable binary run file.
I have created an archive [1] with files demonstrating the problem.
Use the "run" script for a stepwise demonstration of the problem: The
output of mdrun shows that the last frame processed is one less then
expected for concatenated files. Further, it is the second frame that
is missing which can be determined by looking at the energy values in
the energy file generated by mdrun.
I have no clue what is going on here. I hope someone can provide some
insights. (The same approach seems to work fine with PDB files instead
of GROMOS-96 files, but there is less precision in PDB files and
because of some irrelevant details it is easier for me to work with
GROMOS-96 files at the moment.)
[1] http://dl.dropbox.com/u/2666968/GROMACS/missingframe.tar
Thanks,
Martin.
That's a bug. Reading the .g96 file format as a trajectory uses some
dirty dirty non-thread-safe code, and the cleanup a few years ago to
make things thread-safe did that without preserving correct
functionality. I suggest you concatenate separate .g96 files using
trjcat into .trr format, and use rerun on that.
Mark
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