[gmx-users] g_msd

[ram ram]

Dear users,

I am trying to calculate the diffusion coefficient for my protein using
g_msd. I issued the following command:

g_msd -f .xtc -s .pdb  -o .xvg

It gave me the diffusion coefficient as 0.068 (+/- 0.0279) * 10^-5 cm^2 s^
-1  (for my whole system). The shape of the plot is not linear rather it is
parabola (I think it might be due to the short period of simulation but I am
not sure)

I also used g_analyze with the following commad:

g_analyze -f .xvg (the xvg from g_msd I have used here) -msd

This plot is linear but it considered only upto 5ns time period though my
xtc/xvg file contains 10ns data. Could some one tell me why g_analyze
considered only 5ns simulation time. Also how g_msd and g_analyze are
different ?

I learnt form one of Xavier Periole's postings, that g_msd is the
instantaneous value of msd and g_analyze is the average over the entire
simulation. The diffusion coefficient value I got
is from g_msd, how can I calculate the value of the same by using g_analyze
?

Also, while calculating diffusion coefficient, is it better to monitor a
particular atom or a group of atoms or entire protein ?

Thanks and Regards.
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