Calculate MSDs during MD run

Johannes Wagner joh... at
Fri Jul 31 11:02:19 UTC 2015

Hello all,

I was wondering if it was possible to calculate the mean square 
displacement per kind during an MD run and I found REFTRAJ in the reference.
However, if I understand it correctly, I need to already have a trajectory 
for REFTRAJ, is that correct? So basically, do a normal MD, save the 
trajectory and restart the run, pointing to the Trajectory.

But can I somehow calculate the MSD per Kind in regular intervals with a 
fresh MD run simultaniously? So calculating the MSD every 10 steps or so 
with reference to the input structure and have an ouput file printed for 

Thanks for any hints, best regards,
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