[gmx-users] Re: Frame/conformation in trajectory is ignored

Martin Kamp Jensen martin.kamp.jensen at gmail.com
Fri Jul 15 11:31:11 CEST 2011


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

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