[gmx-users] Regarding OH, HH vector distribution

[David van der Spoel]

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
>>>>>>>> --
>>>>>>>> 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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>>>>>>
>>>>
>>>>
>>>> --
>>>> 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
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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
>>
>> * Please search the archive at
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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