gmx msd appears broken in master
gmx msd results in a bunch of nans. The first value (lag = 0, so msd=0) is fine, as is the second. From the third on are nan.
Reproduced with multiple option combinations, with different systems on different machines. Release 2018 is fine.
Uploaded an example of a cg water system. gmx msd -f topol.xtc -s topol.tpr