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

[Mark Abraham]

On 4/01/2012 7:12 PM, Kiwoong Kim wrote:
> 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).

I doubt that "-z" is an acceptable argument. Use "z".

> 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 ??

g_msd will work on whatever set of atoms you choose. You may wish to 
make some custom index groups.

>
> 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 ???

Only if you have covalent bonds in a molecule whose topology is 
infinite. See manual 7.3.9

Mark

>
> please help...
>
> Thank you for reading this lengthy story.
>
>

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