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

rose rahmani rose.rhmn93 at gmail.com
Wed Sep 12 20:02:44 CEST 2018 

On Wed, Sep 12, 2018 at 9:15 PM João Henriques <joao.m.a.henriques at gmail.com>
wrote:

> Did you try with gmx gangle again, after my reply?

yes.

 gmx gangle -f umbrella0.xtc -s umbrella0.tpr -n index.ndx -g1 plane -g2
plane -group1 -group2 -oh -oav

Available static index groups:
 Group  0 "System" (4336 atoms)
 Group  1 "Other" (760 atoms)
 Group  2 "ZnS" (560 atoms)
 Group  3 "WAL" (200 atoms)
 Group  4 "NA" (5 atoms)
 Group  5 "CL" (5 atoms)
 Group  6 "Protein" (26 atoms)
 Group  7 "Protein-H" (12 atoms)
 Group  8 "C-alpha" (1 atoms)
 Group  9 "Backbone" (5 atoms)
 Group 10 "MainChain" (7 atoms)
 Group 11 "MainChain+Cb" (8 atoms)
 Group 12 "MainChain+H" (9 atoms)
 Group 13 "SideChain" (17 atoms)
 Group 14 "SideChain-H" (5 atoms)
 Group 15 "Prot-Masses" (26 atoms)
 Group 16 "non-Protein" (4310 atoms)
 Group 17 "Water" (3540 atoms)
 Group 18 "SOL" (3540 atoms)
 Group 19 "non-Water" (796 atoms)
 Group 20 "Ion" (10 atoms)
 Group 21 "ZnS" (560 atoms)
 Group 22 "WAL" (200 atoms)
 Group 23 "NA" (5 atoms)
 Group 24 "CL" (5 atoms)
 Group 25 "Water_and_ions" (3550 atoms)
 Group 26 "Protein" (26 atoms)
 Group 27 "ZnS" (560 atoms)
 Group 28 "ZnS" (560 atoms)
Specify any number of selections for option 'group1'
(First analysis/vector selection):
(one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
> 17
Selection '17' parsed
> 27
Selection '27' parsed
> Available static index groups:
 Group  0 "System" (4336 atoms)
 Group  1 "Other" (760 atoms)
 Group  2 "ZnS" (560 atoms)
 Group  3 "WAL" (200 atoms)
 Group  4 "NA" (5 atoms)
 Group  5 "CL" (5 atoms)
 Group  6 "Protein" (26 atoms)
 Group  7 "Protein-H" (12 atoms)
 Group  8 "C-alpha" (1 atoms)
 Group  9 "Backbone" (5 atoms)
 Group 10 "MainChain" (7 atoms)
 Group 11 "MainChain+Cb" (8 atoms)
 Group 12 "MainChain+H" (9 atoms)
 Group 13 "SideChain" (17 atoms)
 Group 14 "SideChain-H" (5 atoms)
 Group 15 "Prot-Masses" (26 atoms)
 Group 16 "non-Protein" (4310 atoms)
 Group 17 "Water" (3540 atoms)
 Group 18 "SOL" (3540 atoms)
 Group 19 "non-Water" (796 atoms)
 Group 20 "Ion" (10 atoms)
 Group 21 "ZnS" (560 atoms)
 Group 22 "WAL" (200 atoms)
 Group 23 "NA" (5 atoms)
 Group 24 "CL" (5 atoms)
 Group 25 "Water_and_ions" (3550 atoms)
 Group 26 "Protein" (26 atoms)
 Group 27 "ZnS" (560 atoms)
 Group 28 "ZnS" (560 atoms)
Specify any number of selections for option 'group2'
(Second analysis/vector selection):
(one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
> 17
Selection '17' parsed
> 27
Selection '27' parsed
> Reading file umbrella0.tpr, VERSION 4.5.4 (single precision)
Reading file umbrella0.tpr, VERSION 4.5.4 (single precision)

-------------------------------------------------------
Program:     gmx gangle, VERSION 5.1.4
Source file: src/gromacs/trajectoryanalysis/modules/angle.cpp (line 468)
Function:    void
gmx::analysismodules::{anonymous}::Angle::initFromSelections(const
SelectionList&, const SelectionList&)

Inconsistency in user input:
Number of positions in selection 2 in the first group not divisible by 3

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Before writing code you
> should always make sure that what is at hand can't do the job first.
>
> Also, I've already directed you to an example in my previous email. Check
> the MDAnalysis link again. If Python isn't your thing, feel free to use any
> other language. Even the PLUMED driver could do the trick with some work.
>
> J
>
>
>
>
> On Wed, Sep 12, 2018 at 6:04 PM Nick Johans <johans.nick93 at gmail.com>
> wrote:
>
> > 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
> > >> > > > > > --
> > >> > > > > > Gromacs Users mailing list
> > >> > > > > >
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> > >> > > > > > posting!
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