[gmx-users] Regarding OH, HH vector distribution

[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


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
> >> --
> >> Gromacs Users mailing list
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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
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