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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jul 15 13:41:21 CEST 2011

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.

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