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).
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