[gmx-users] g_msd

Arneh Babakhani ababakha at mccammon.ucsd.edu
Fri Sep 1 22:19:44 CEST 2006

Hi everyone, quick question about g_msd,

When I execute:   *g_msd -f FullMD1.trr -s FullMD1.tpr -n 
ForDiffusion.ndx -o test -lateral z*

At the end, the following is outputted in my terminal:

*D[   Protein] 0.1207 (+/- 0.0847) 1e-5 cm^2/s*

My index file only contains one group, labeled Protein.  So is this 
number, *0.1207*, the MSD of the entire group Protein? Or is this the 
average (over the atoms) MSD in the group Protein?  (I think the latter 
is the case, b/c in the manual, it's stated that g_msd computes the MSD 
of atoms . . . just double-checking).

Thanks much,


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