[gmx-users] how to plot g_msd in one direction?

Kiwoong Kim ilmarekw at gmail.com
Wed Jan 4 09:12:20 CET 2012

Dear members of gromacs

I have several questions.

I have been working on the diffusion problem (diffusing particles diffuse
into the zeolite).

Although I have successfully obtained the output file, there are problems
for analyzing it.

My questions are

1) I have to calculate diffusion coefficient using g_msd. To my knowledge,
the directional diffusion coefficient can be acquired by -type -z (for
But, it seems that the plot of MSD using g_msd is the result of 3
dimensionally averaged MSD but not z direction.
How can I produce the MSD graph which has only uni-directional information.
(ignore x, y displacement. only account for z-directional displacement)

2) There are 20-30 particles as diffusing particles. g_msd, of course,
compute the averaged MSD for whole particles. Is it true??
Then, how can I obtain the MSD graph for only single particle ??

3) in mdp file, there is option for periodic_molecules. I couldn't
understant how it is working.
In my system ( assumed to be infinite zeolite), do I have to set the
periodic_molecules = yes ???

please help...

Thank you for reading this lengthy story.
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