Have you ever been trying to analyze a simulation that you KNOW worked, but for some reason the analysis script that worked on every other replicate isn’t working for one of them? And then you go to look at it and there are frames that are missing? No? Just me? Fine. If you did, though, your cpptraj log (or error file or wherever you get the cpptraj information printed to) may have this message:

Warning: Frame XXXX coords 1 & 2 overlap at origin; may be corrupt.

This can mean a few things, including but not limited to, a corrupted simulation (the horror). If you had rewritten the trajectory, though, it could just mean that the rewrite was corrupted. Corruption can happen for all sorts of reasons, like input/output errors, problems with the computer just because it’s a computer, random losses of power… you get the idea.

Here’s two things that may fix the problem.

  1. Try rewriting the trajectory again.
  2. Rerun cpptraj with the check skipbadframes option. (You may be shocked that this skips frames that aren’t good.)