[gmx-users] Regarding OH, HH vector distribution

[David van der Spoel]

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
>>>> --
>>>> 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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-- 
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