[gmx-users] Regarding mean square displacement

Kavyashree M hmkvsri at gmail.com
Wed Feb 6 11:05:48 CET 2013

Dear users,

 I have a very basic question in MSD calculation.
g_msd calculation on a protein dimer (~237 aa each)
trajectory gave a plot of msd, with the values ranging
between 1 to 14nm^2.
But is this a sensible MSD? As the values given in a
paper i was referring was in Ang^2
J. Chem. Theory Comput. 2012, 8, 1129-1142

Command that i used -

echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000 -e
50000 -rmcomm

Is the range of diffusion coefficient of proteins of in water l
in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)

Thank you

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