[gmx-users] Regarding OH, HH vector distribution

[Omkar Singh]

I calculated these two vectors with Z-axis  now I want to  make
distribution plot p(costheeta) Vs cos(theeta). How can I plot because it is
giving the value only theeta. Is there any command.
Thanks

On Wed, Jul 31, 2019, 12:00 David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> Den 2019-07-31 kl. 06:12, skrev Omkar Singh:
> > Thanks Sir,
> > I did like that only, Now how can I make the distribution plot for these
> > vectors. Eventhough I used "gmx analyze -f .xvg     -dist .." command.
> But
> > results is not proper. Can you suggest me regarding this?
> > Thank you
> >
> How about gmx gangle -oh ?
>
> >
> > On Tue, Jul 30, 2019, 17:27 David van der Spoel <spoel at xray.bmc.uu.se>
> > wrote:
> >
> >> Den 2019-07-30 kl. 07:55, skrev Omkar Singh:
> >>> Hi,
> >>> I did by  "gmx gangle ..." command. But I am not getting good result,
> >>> because I have a doubt in ndx file.  Can you help me for making  ndx
> >> file.
> >>> How should I select the atom for vectors.
> >> For OH it should be
> >> 1 2
> >> 1 3
> >> 4 5
> >> 4 6
> >> 7 8
> >> 7 9
> >> etc., assuming a three particle water model with atoms O H H.
> >> For HH it should be
> >> 2 3
> >> 5 6
> >> 8 9
> >> etc.
> >> A simple script would do it. The dipole vector is somewhat harder.
> >>> Thanks
> >>>
> >>> On Mon, Jul 29, 2019, 22:50 David van der Spoel <spoel at xray.bmc.uu.se>
> >>> wrote:
> >>>
> >>>> Den 2019-07-29 kl. 18:26, skrev Omkar Singh:
> >>>>> Hi,
> >>>>> Meaning is that If I want to calculate angle between OH, HH and dip
> >>>> vector
> >>>>> with positive Z-axis. How can I make index file for this issue? And
> is
> >> it
> >>>>> possible that the angle distribution of these vectors for bulk water
> >>>>> aproximatly linear. Hope now question is clear.
> >>>> Probably. Check gmx gangle -g2 z
> >>>>>
> >>>>> Thanks
> >>>>>
> >>>>> On Mon, Jul 29, 2019, 16:33 David van der Spoel <
> spoel at xray.bmc.uu.se>
> >>>>> wrote:
> >>>>>
> >>>>>> Den 2019-07-29 kl. 12:24, skrev Omkar Singh:
> >>>>>>> Hello everyone,
> >>>>>>> Is it possible that the probability distribution of HH, OH vector
> for
> >>>>>> bulk
> >>>>>>> water is approximately linear?
> >>>>>>>
> >>>>>> What do you mean?
> >>>>>>
> >>>>>> --
> >>>>>> David van der Spoel, Ph.D., Professor of Biology
> >>>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
> >>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> >>>>>> http://www.icm.uu.se
> >>>>>> --
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> >>>>
> >>>>
> >>>> --
> >>>> David van der Spoel, Ph.D., Professor of Biology
> >>>> Head of Department, Cell & Molecular Biology, Uppsala University.
> >>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> >>>> http://www.icm.uu.se
> >>>> --
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> >>
> >>
> >> --
> >> David van der Spoel, Ph.D., Professor of Biology
> >> Head of Department, Cell & Molecular Biology, Uppsala University.
> >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> >> http://www.icm.uu.se
> >> --
> >> 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-request at gromacs.org.
> >>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> Gromacs Users mailing list
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