[gmx-users] msd vs. time plot for molecules

Michael Skaug mjskaug at ucdavis.edu
Fri Jun 20 20:30:59 CEST 2008

Using g_msd on a group of atoms results in an msd vs. time plot which is 
the result of an average over all the atoms' motions.  I would like to 
obtain the same plot, but for an average over the center of mass motions 
of a group of molecules.  Using the -mol option results in a plot of the 
diffusion coefficient for each individual molecule.  Do I need to use 
the -mw option for each molecule seperately and then average them 
together myself?  Thank you for any ideas.

--Mike Skaug

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