Error while trying to reorder trajectory

[markohanzevacki]

When trying to run reorder_trj.py script we get this following error and it occurs in at least two different systems:

"Error: NetCDF file has no frames.
Error: Could not set up '.reorder_trj_tmp/17_87.nc' for reading.
Error: Could not set up input trajectory '.reorder_trj_tmp/17_87.nc'.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
leError: NetCDF file has no frames.
Error: Could not set up '.reorder_trj_tmp/18_89.nc' for reading.
Error: Could not set up input trajectory '.reorder_trj_tmp/18_89.nc'.
1 errors encountered reading input.
Error: Error(s) occurred during execution. Error: NetCDF file has no frames.
Error: Could not set up '.reorder_trj_tmp/19_84.nc' for reading.
Error: Could not set up input trajectory '.reorder_trj_tmp/19_84.nc'.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
Error: NetCDF file has no frames.
Error: Could not set up '.reorder_trj_tmp/20_82.nc' for reading.
Error: Could not set up input trajectory '.reorder_trj_tmp/20_82.nc'.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
Error: NetCDF file has no frames........"

The output directory which should contain reordered trajectories typically contains only reordered string phase but one, few or none files for pmf phase.

This is due to last trajectories that the script is trying to combine seem not to have any frames.

Because of that we can't run get_ts_frames.py or resume US phase.

Any suggestions?

Thank you,

Marko

[kzinovjev]

Hi,

I see, probably two replica exchanges happened too fast, so that only a single frame was written to the trajectory file. Would it be possible for you to share the nc files? How large are these?

If I'm right, a quick "fix" would be to either decrease the period at which the frames are written to the nc files (ntwx in the sander input) or to increase the period of replica exchange attempts (REX_period in the STRING file).