Sorry, hit send accidentally. Continuing,
So the question is, what is the correct way of doing what I want? Would
fix 3 all msd 100 diffsquared.1 com yes
fix 4 all msd 100 diffsquared.2 com yes
work? I assume I have to get rid of the fix recenter, but not fixes 3 and 4 will each subtract out the COM motion relative to the time they were called. Then, if I have to remove the COM motion for other data analysis, I can always do it in postprocessing rather than the fix recenter. Should this be OK? Are there any other issues with msd fixes at multiple time origins (and multiple “run” commands) I should know about?