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

Wed Sep 12 18:03:38 CEST 2018

Sorry i'm nick's friend and i couldn't access to my email so i had to send
it by his account.

Rose

On Wed, 12 Sep 2018, 20:16 Nick Johans, <johans.nick93 at gmail.com> wrote:

> 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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