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On 4/01/2012 7:12 PM, Kiwoong Kim wrote:
<blockquote
cite="mid:CALmcptDOgn7w3ifZtD-V1PcSyxkg=Hbw5gaiK8L-xxfBKfNQ5w@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
I doubt that "-z" is an acceptable argument. Use "z".<br>
<br>
<blockquote
cite="mid:CALmcptDOgn7w3ifZtD-V1PcSyxkg=Hbw5gaiK8L-xxfBKfNQ5w@mail.gmail.com"
type="cite">
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>
</blockquote>
<br>
g_msd will work on whatever set of atoms you choose. You may wish to
make some custom index groups.<br>
<br>
<blockquote
cite="mid:CALmcptDOgn7w3ifZtD-V1PcSyxkg=Hbw5gaiK8L-xxfBKfNQ5w@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
Only if you have covalent bonds in a molecule whose topology is
infinite. See manual 7.3.9<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CALmcptDOgn7w3ifZtD-V1PcSyxkg=Hbw5gaiK8L-xxfBKfNQ5w@mail.gmail.com"
type="cite">
<br>
please help... <br>
<br>
Thank you for reading this lengthy story. <br>
<br>
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<br>
</blockquote>
<br>
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