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

João Henriques joao.m.a.henriques at gmail.com
Wed Sep 12 20:46:53 CEST 2018 

Ok, that's not a gromacs problem, that's you not understanding what you are
doing in regard to the selections. You can't just pass all the atoms of all
water molecules and all the atoms of your surface and expect gromacs to
define the planes for you. What I meant in my simple example was that you
should try passing 3 atoms on your surface to define a reference plane and
3 atoms on a single water molecule to define its H-O-H plane. Then see if
it runs. If it does, then it's time to think about how you can do that for
all water molecules in the system. Do you follow me?

Unless you plan on defining these points in a .ndx file, I suggest you get
familiar with the selection syntax:

http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html

J

On Wed, Sep 12, 2018 at 8:04 PM rose rahmani <rose.rhmn93 at gmail.com> wrote:

> 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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