Is there any smart way to continue a run that crashed?
Yes, if the reason for the crash didn’t have anything to doe with the algorithms, i.e. it was due to a system crash, a full disk, or a kill by the queuing system. Otherwise you’ll have to use grompp and change the options. To really continue a simulation as if nothing had happened, you will need coordinates and velocities in full precision (i.e. .trr format). .xtc trajectories are in reduced precision (only 3 decimal places after the decimal point) and do not contain velocity information at all. Feed this trajectory and your origional .tpr file to tpbconv to obtain a new .tpr file, be sure to specify the one-but-last frame from your .trr file, since the very last frame is likely to be corrupted due to the crash. With the .tpr file tpbconv produces you can restart your simulation. After the continuation run is finished, you will have your simulation split up in separate files, which you will probably want to combine.
