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Hi everyone, quick question about g_msd, <br>
<br>
When I execute: <b>g_msd -f FullMD1.trr -s FullMD1.tpr -n
ForDiffusion.ndx -o test -lateral z</b><br>
<br>
At the end, the following is outputted in my terminal: <br>
<br>
<b>D[ Protein] 0.1207 (+/- 0.0847) 1e-5 cm^2/s</b><br>
<br>
My index file only contains one group, labeled Protein. So is this
number, <b>0.1207</b>, 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).<br>
<br>
Thanks much, <br>
<br>
Arneh <br>
<br>
<br>
<br>
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