GROMACS modification: No
I am having problems using trjcat with chunks of a long simulation, where it seems to drop a handful (tens) of frames at the boundaries between chunks, leaving gaps in the trajectory .trr. Since this problem does not occur for shorter simulations, I suspect that the problem is that trjcat uses the timestamps to match up frames, but the recorded times become unstable for trajectories with large numbers of steps. All I really need to do is manually remove the first frame from each chunk and then I could just do an ordinary cat. But looking at the options for gmx trjconv, I see no way to simply remove the first frame without specifying it’s time, which as I noted is iffy. I should note that I need to work with the .trr format as I am recording velocities and forces.
Is there any simple way to remove the first frame from a trajectory without knowing it’s timestamp? I could of course try to gmx dump the output and then do it manually, but that seems clunky and I would like to avoid unnecessary duplication of data since I have large files.