"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.henriq...@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.rhm...@gmail.com> > wrote: > >> On Wed, 12 Sep 2018, 19:13 João Henriques, <joao.m.a.henriq...@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.rhm...@gmail.com> >> > wrote: >> > >> > > Thank you Joao, >> > > >> > > On Wed, 12 Sep 2018, 14:04 João Henriques, < >> joao.m.a.henriq...@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.rhm...@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 >> > > > > >> > > > > * Please search the archive at >> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >> before >> > > > > posting! >> > > > > >> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > >> > > > > * For (un)subscribe requests visit >> > > > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> > or >> > > > > send a mail to gmx-users-requ...@gromacs.org. >> > > > > >> > > > -- >> > > > Gromacs Users mailing list >> > > > >> > > > * Please search the archive at >> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > > > posting! >> > > > >> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > >> > > > * For (un)subscribe requests visit >> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or >> > > > send a mail to gmx-users-requ...@gromacs.org. >> > > -- >> > > Gromacs Users mailing list >> > > >> > > * Please search the archive at >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > > posting! >> > > >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > >> > > * For (un)subscribe requests visit >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > > send a mail to gmx-users-requ...@gromacs.org. >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.