any attempt to replace the part of input script above the "Main run" section with the
read_restart command results in continued execution from the proper place where
it stopped. However, MSD file will contain only zeros. If I understood correctly
the "compute msd" should be restartable, but "compute msd/molecule" is not?
If this is so, how come my "compute msd" is lacking the initial coordinates information
which is I believe main cause why restarted MSD is not continuing to append the proper
values to the existing MSD file. Am I restarting it in a wrong way perhaps?
The list of fixes used for a simulation is not stored in the restart
file. This means the new input script should specify all fixes it will
use. Note that some fixes store an internal "state" which is written
to the restart file. This allows the fix to continue on with its
calculations in a restarted simulation. To re-enable such a fix, the
fix command in the new input script must use the same fix-ID and
group-ID as was used in the input script that wrote the restart file.
If a match is found, LAMMPS prints a message indicating that the fix
is being re-enabled. If no match is found before the first run or
minimization is performed by the new script, the "state" information
for the saved fix is discarded. See the doc pages for individual fixes
for info on which ones can be restarted in this manner.
Compute msd uses the fix store/state command, so if
you specify the same ID for the compute, it should generate
the same ID for the fix and thus restart with old info restored.
Are you getting the printed message that the fix is re-enabled?