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

Martin Kamp Jensen martin.kamp.jensen at gmail.com
Sat Jul 16 12:33:52 CEST 2011

On Fri, Jul 15, 2011 at 1:41 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> **
> 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.

Too bad, but thank you for explaining. Is your suggestion based on the fact
that the functionality is completely unreliable? I mean, if the bugs are
known (e.g. 2nd frame is always ignored), it would maybe be better to just
work around them. (It would be a bit sad to write out 100 or 1000 g96 files
and then use trjcat since I will need to do that millions of times during a
run of my application.)


> Mark
> --
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