[gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[João Henriques]

"It gives me the histogram of angles" ---> what is "it" in this sentence?
There are 26 emails on the link I shared. What did you actually try? I
mean, an histogram and a distribution function aren't that far apart...
Also, I believe understand what you want to do, you want to calculate the
ADF of the water molecules with the protein surface as the reference. Something
like this <https://pubs.acs.org/doi/abs/10.1021/jp0604241> (see Figures 3
and 5). Well, I've played around with a similar problem and there's no
simple answer. I ended up using MDAnalysis
<https://www.mdanalysis.org/docs/documentation_pages/analysis/waterdynamics.html>
(click on the link, see 4.8.3.1.3. AngularDistribution). I tried doing the
same with the native Gromacs tools but found it too be too much of a pain
in the a**.

I hope this is at least somewhat useful.

Cheers,
João



On Wed, Sep 12, 2018 at 3:41 PM rose rahmani <rose.rhmn93 at gmail.com> wrote:

> Thank you Joao,
>
> On Wed, 12 Sep 2018, 14:04 João Henriques, <joao.m.a.henriques at gmail.com>
> wrote:
>
> > Dear Rose,
> >
> > Spamming is not the answer. There have been quite a few threads about
> this
> > subject in the recent past. Searching the mailing list before posting is
> > usually good practice. If then something remains unclear, please feel
> free
> > to ask. I remember having quite long discussions with a Dilip H. N. about
> > this subject (on and off the mailing list).
> >
> > A simple query fetched 26 results:
> >
> >
> https://www.mail-archive.com/search?l=gromacs.org_gmx-users%40maillist.sys.kth.se&q=dilip+h+n+angle&x=0&y=0
>
> I search and read about but it didn't help me. It gives me the histogram of
> angles but what i really want is the distribituion of special defined
> angle(between two plane) during simulation. I refer you ahain to
>
> https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface?_ec=topicPostOverviewAuthoredQuestions&_sg=hV7QNgmmW-MkZF5OKfgZlaI5O0G5HeVQGSGoneQ1gDaXV_96qBhs2Re6IrsBNcXYMTf0FzIqXPyDrI9r.8ylTJZVEy00BT4mPuq0m2nGK5dREPBjukd2plNMaXf5ocFCOJCRriPhzJum_Vt2KLoZVmTZVBDoQZQOcBKAP8EU
>
>
> https://www.researchgate.net/post/How_can_i_calculate_the_distribution_of_water_polarization_above_surface
>
>  I asked different questions several times last 2 days and i thought my
> email doesn't recieve and share in mailing-list.
>
> I'm really confused about what people suggest. I'm a student and i think, i
> clearly explained what i want after huge searches, it's not because of
> indolence and i would be appreciated if any one could answer me.
>
> Regards
>
>
>
> > Play with the query a bit and it should get you a lot of info on your
> > problem.
> >
> > Best regards,
> > João
> >
> >
> >
> >
> >
> > On Mon, Sep 10, 2018 at 10:29 AM rose rahmani <rose.rhmn93 at gmail.com>
> > wrote:
> >
> > > Hi,
> > > How can i calculate the angular distribution of the angles between
> water
> > > molecule water and surface? surface during molecular dynamics
> simulation?
> > >  is it possible by GROMACS? gmx gangle?
> > >
> > > would you please help me?
> > >
> > > To be clear; i refer you to these plots
> > >
> > >
> >
> https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface
> > >
> > >
> > > Best regards
> > >
> > > Rose
> > > --
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