Is MSD single particle or all particle?

Dear Forum users

I have overall seen different definitions of the mean squared displacement (MSD), some avarage over time for a single particle, while others also average over all particles of the system.

Which case is the command “gmx msd”?

Regards

Sotadebastos

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-msd.html

That depends on what your selection is when you execute the command, via the index groups (generated by gmx or otherwise in the index.ndx file).