Dear members of gromacs<br>
<br>
I have several questions.<br>
<br>
I have been working on the diffusion problem (diffusing particles diffuse into the zeolite).<br>
<br>
Although I have successfully obtained the output file, there are problems for analyzing it.<br>
<br>
My questions are<br>
<br>
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). <br>
But, it seems that the plot of MSD using g_msd is the result of 3 dimensionally averaged MSD but not z direction.<br>
How can I produce the MSD graph which has only uni-directional
information. (ignore x, y displacement. only account for z-directional
displacement) <br>
<br>
2) There are 20-30 particles as diffusing particles. g_msd, of course,
compute the averaged MSD for whole particles. Is it true??<br>
Then, how can I obtain the MSD graph for only single particle ?? <br>
<br>
3) in mdp file, there is option for periodic_molecules. I couldn't understant how it is working. <br>
In my system ( assumed to be infinite zeolite), do I have to set the periodic_molecules = yes ???<br>
<br>
please help... <br>
<br>
Thank you for reading this lengthy story. <br>