[gmx-users] Timesteps don't match

[Alexander Peyser]

Dear all,

I'm receiving a "timesteps don't match" error, due to a wobble in the time
between steps for my xtc trajectory file. The source of the wobble is
mysterious.

I'm running gromacs-4.5.5 with plumed patches for a very long trajectory
using double precision code with a time step of 2fs and xtc frames every
200fs. The trajectory was run in 24 hour chunks, with a continuation with
-append over all the chunks. The timing fit precisely the values set over
many, many chunks.

Unfortunately, I was trying to consolidate some disk space and lost my log
file, which kept me from simply running mdrun_d with -append to continue
the trajectory as I had been doing. I started a new trajectory with the
checkpoint file by extending the tpr with tpbconv, and then continued
appending to the output from that. The beginning time is correct, beginning
right after the end of the first trajectory. However, every frame is
separated from the next by 187.5 fs or 218.75 fs, repeatedly. I've checked
my input files, my cpt checkpoint and my tpr run file --- there are no step
values like that at all, and the xtc output time continues to be set as
every 100 steps, with a step time of 2fs.

Where should I look to identify the source of this wobble? Has anyone seen
anything similar?

Alex Peyser