[gmx-users] Gmx gangle

[rose rahmani]

Sorry,
BTW, the slab is in xy plane. But i get an error when i use -g2 y or x .

How should i define the surface plane?

On Sun, 9 Sep 2018, 14:45 rose rahmani, <rose.rhmn93 at gmail.com> wrote:

> Hi,
>
> I want to calculate angle between water molecules and ZnS surface(slab). I
> mean the angular distribution function(ADF) of ALPHA and BETA. I define to
> angles; Alpha= angle between OH bond of water and  surface(plane)    Beta=
> angle between HOH plane and surface(plane).
>
> I used gmax gangle for Alpha:
> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh
> Then i selected water(SOL) group
>
> For Beta:
> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh
> And again i selected water group.
>
> But results are little odd and histograms are two plot which are symmetric
> plots.
>
> I think sth is wrong. Should i make an index file for OH bond in the case
> of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it
> calculated the angle between COM of water vector and surface not the OH
> bond of water. As you know water has 2 OH bond. So... what should i do?
>
> How about BETA? does it really calculate what i want?
>
> Should i make an special index file?
>
> If i want to calculate this property (ADF) in for example 1 nm from
> surface, what should i do?
>
> To be more clear, I refer you to fig.1 and fig.8
> roja:
>
> https://www.researchgate.net/publication/257760740_Structural_properties_of_water_around_uncharged_and_charged_carbon_nanotubes/figures
>
> Would you please help me how can i reach these goals?
>
> Best regards
>
> Rose
>
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