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

Wed Sep 12 17:35:47 CEST 2018

"being that the reference is a surface" ---> I meant a "planar surface"

J

On Wed, Sep 12, 2018 at 5:34 PM 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).
>>
>> 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
>> > > > > --
>> > > > > Gromacs Users mailing list
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