[gmx-users] dipole on an atom

[Faezeh Pousaneh]

I think I have my answer to my initial question; how to give an atom a
dipole? One can use virtual sites.


Best regards


On Mon, Nov 6, 2017 at 3:03 PM, Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> David,
> do you thin that Stockmayer potential can be implemented by user-specified
> potential?
>
>
> Best regards
>
>
> On Sun, Nov 5, 2017 at 4:18 PM, David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
>
>> On 05/11/17 16:07, Faezeh Pousaneh wrote:
>>
>>> Yes, exactly. But my atom is uncharged sphere, I'll bring two similar
>>> size
>>> and similar mass (+ -) ions inside the sphere. So rotation will not
>>> happen
>>> then for atom.
>>>
>>
>> If you simulate multiple such spheres they will behave like a Stockmayer
>> dipolar fluid.
>>
>>
>>>
>>> On Nov 5, 2017 16:00, "David van der Spoel" <spoel at xray.bmc.uu.se>
>>> wrote:
>>>
>>> On 05/11/17 15:54, Faezeh Pousaneh wrote:
>>>
>>> So I guess the only solution can be:
>>>>
>>>> I take two small ions bring them inside original atom, parametrize their
>>>> interactions with each other and the initial atom such that they stick
>>>> inside the atom.
>>>> What do you think?
>>>>
>>>> In fact you are then creating a small molecule, like C=O. Nothing wrong
>>> with that, but you are also creating particles with a mass, which means
>>> the
>>> "atom" get rotational properties.
>>>
>>>
>>>
>>>
>>>
>>>> Best regards
>>>>
>>>>
>>>> On Sun, Nov 5, 2017 at 3:42 PM, David van der Spoel <
>>>> spoel at xray.bmc.uu.se>
>>>> wrote:
>>>>
>>>> On 04/11/17 19:19, Faezeh Pousaneh wrote:
>>>>
>>>>>
>>>>> Hi,
>>>>>
>>>>>>
>>>>>> I have an uncharged atom, and I would like to give it a dipole. Any
>>>>>> suggestion?
>>>>>>
>>>>>> impossible in gromacs.
>>>>>>
>>>>>
>>>>>
>>>>> Best regards
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>> 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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>
>