I tried to use the compute MSD command for water molecules in LAMMPS.
I then used the following fix to get the MSD.
"fix 1 all ave/time 10 10 100 c_1 ave running start 10 file water.msd mode vector".
The simulation ran without any problem. But whenever i try to restart the simulation with a restart file,
the MSD are higher than the one at the last step of the previous run.
Could you kindly let me solve this issue.
Thanks in advance
If you mean the values in the fix ave/time file are discontinuous
across the restart, then I don't see why they should be
continuous. Fix ave/time doesn't save any into to
the restart file. And you are using a "running" ave. So the
first output in the 2nd run knows nothing about the accumulated
ave over the 1st run.
I should add that the usual point of calculating an MSD
is to produce a plot of MSD vs time. To do that
you do not want a "running" ave output by fix ave/time.
That will mean every output value is the average of
all the previous-time MSD values.
Thanks for the information.
But, though they are discontinuous, the slope the curve remains pretty much
the same but with a shift of certain order of magnitude. On replotting removing the order
of shift, the plot looks fine. However, I understand that the usage of "running" ave was not a
good idea. Thanks again,