[gmx-users] Regarding OH, HH vector distribution

[David van der Spoel]

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