Is sth wrong or unclear in my question?😔
On Sun, 9 Sep 2018, 15:01 rose rahmani, <rose.rhm...@gmail.com> wrote: > Sorry, > BTW, the slab is in xy plane. But i get an error when i use -g2 y or x . > > How should i define the surface plane? > > On Sun, 9 Sep 2018, 14:45 rose rahmani, <rose.rhm...@gmail.com> wrote: > >> Hi, >> >> I want to calculate angle between water molecules and ZnS surface(slab). >> I mean the angular distribution function(ADF) of ALPHA and BETA. I define >> to angles; Alpha= angle between OH bond of water and surface(plane) >> Beta= angle between HOH plane and surface(plane). >> >> I used gmax gangle for Alpha: >> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh >> Then i selected water(SOL) group >> >> For Beta: >> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh >> And again i selected water group. >> >> But results are little odd and histograms are two plot which are >> symmetric plots. >> >> I think sth is wrong. Should i make an index file for OH bond in the case >> of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it >> calculated the angle between COM of water vector and surface not the OH >> bond of water. As you know water has 2 OH bond. So... what should i do? >> >> How about BETA? does it really calculate what i want? >> >> Should i make an special index file? >> >> If i want to calculate this property (ADF) in for example 1 nm from >> surface, what should i do? >> >> To be more clear, I refer you to fig.1 and fig.8 >> roja: >> >> https://www.researchgate.net/publication/257760740_Structural_properties_of_water_around_uncharged_and_charged_carbon_nanotubes/figures >> >> Would you please help me how can i reach these goals? >> >> 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.
