[gmx-users] Gmx gangle

[rose rahmani]

Is sth wrong or unclear in my question?😔


On Sun, 9 Sep 2018, 15:01 rose rahmani, <rose.rhmn93 at gmail.com> wrote:

> 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
>>
>>
>>
>>
>>