[gmx-users] Tetrahedral order parameter

[Omkar Singh]

Hi all gmx-users,
I have a water-protein simulated  system. I  want to calculate the
Tetrahedral order parameter. Can anybody help me regarding this issue.


On Thu, Aug 1, 2019, 00:52 David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> Den 2019-07-31 kl. 15:00, skrev 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.
> Try write your own script.
> > 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
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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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> >> posting!
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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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