On Sun, Sep 19, 2010, Seibold, Stephen wrote:
>
> I am using the newest version of ptraj and have applied all the
> bugfixes. I am sending you the input and output log file on the
> Distance measurement failure. I would send you my trajectories but they
> are very large. The problem seems to be (so far) only the distance
> measurements. For example, calculating RMSD does not appear to be a
> problem.
According to the input file, you ran 200,000 steps, dumping coordinates every
5000 steps, so there should be 40 frames in the trajectory. Yet ptraj says:
"Coordinate processing will occur on 38 frames." This sounds like the
trajectory file may be damaged in some fashion.
Things to try:
1. What does "ls -l" report for the trajectory file? (223743790 bytes is what
I expect, based on the ptraj output.) What does running "tail" on the
trajectory file show?
2. Would the job run if you asked it to process just the first 10 or 20
snapshots?
3. Is there anything in the mdout file that points
to a problem near the end of the run?
....dac
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Received on Sun Sep 19 2010 - 18:30:05 PDT
