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 example). 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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