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

Nick Johans johans.nick93 at gmail.com
Wed Sep 12 17:47:09 CEST 2018 

Thank you so much Joao for detailed answer. You are right, i think i should
write my own code. But since i don't have much experience in programming,
would you please introduce me some useful examples?
 And(see below; our former conversations)

Best
Rose
On Wed, 12 Sep 2018, 20:04 João Henriques, <joao.m.a.henriques at gmail.com>
wrote:

> Ok, being that the reference is a surface gmx gangle might work. Notice
> that I wrote might, because I believe it will still be cumbersome for the
> many water molecules in the box. For the example of the two planes, you
> just basically need to set "-g1 plane", "-g2 plane" and pass the selections
> of the surface and water molecule H-O-H plane to "-group1" and "-group2",
> respectively. For the example of the surface and the H-O vector, you adapt
> it accordingly ("-g1 plane", "-g2 vector" and the corresponding
> selections). I easily can see this working for a single water molecule, but
> for all the water molecules in the box this might get tricky. Specially if
> you're gonna try to tackle them all under a single selection. You could
> aways run the command in a loop for each water molecule in the box, but
> that doesn't look very "smart" and/or fast.
>
> I'd still probably look into doing my own code using some third party
> module/package to parse and analyze trajectories.
>
> J
>
> On Wed, Sep 12, 2018 at 5:01 PM rose rahmani <rose.rhmn93 at gmail.com>
> wrote:
>
> > On Wed, 12 Sep 2018, 19:13 João Henriques, <joao.m.a.henriques at gmail.com
> >
> > wrote:
> >
> > > "It gives me the histogram of angles" ---> what is "it" in this
> sentence?
> > >
> > It= -oh output of gmx gangle which writes the histogram of 'angleS' not
> the
> > angle that i have already defined.( THE beta angle= angle between HOH
> plane
> > of water molecules and surface plane , THE alpha angke= angle between OH
> of
> > water molecules and surface plane. The surface is ZnS surface(i have an
> > slab of ZnS) not protein.
> >
> > > 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).
> >
>
How can i use it in gromacs?

> > Thank you.
> >
> > > I tried doing the
> > > same with the native Gromacs tools but found it too be too much of a
> pain
> > > in the a**.
> > >
> > I think gromacs can do it. But first i should define all O-H and in box
> > then calculate the angle between .... for ALPHA
> > Maybe should define H-O-H plane then.... for BETA).
> >
> > I found the documentation of gmx gangle gmx angle so complicated and
> > confusing. I don't know how can i hsethem priperly...
> >
> > Best
> >
> > >
> > > 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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