[gmx-users] dipole on an atom

[Faezeh Pousaneh]

virtual sites plus shell (drude) particle. which unfortunately there is
little information in the manual.


Best regards


On Mon, Nov 6, 2017 at 5:16 PM, Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> 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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>>
>>
>