Re: [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  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 
> 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 > > 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" 
 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 <
> sp...@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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>>

>>>
>>> --
>>> 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 http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>
>>
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [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  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 
> 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" 
>>> 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 <
 sp...@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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>>>
>>
>> --
>> 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 http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] dipole on an atom

[Faezeh Pousaneh]

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 
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"  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 <
>>> sp...@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
 --
 Gromacs Users mailing list

 * Please search the archive at http://www.gromacs.org/Support
 /Mailing_Lists/GMX-Users_List before posting!

 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.



>>
>
> --
> 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 http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] dipole on an atom

[David van der Spoel]

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"  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 
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
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.







--
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 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] dipole on an atom

[Faezeh Pousaneh]

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.


On Nov 5, 2017 16:00, "David van der Spoel"  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 
> 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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>

-- 
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 http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] dipole on an atom

[David van der Spoel]

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 
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
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.




--
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 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] dipole on an atom

[Faezeh Pousaneh]

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?


Best regards


On Sun, Nov 5, 2017 at 3:42 PM, David van der Spoel 
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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] dipole on an atom

[David van der Spoel]

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
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] dipole on an atom

[Faezeh Pousaneh]

Hi,

I have an uncharged atom, and I would like to give it a dipole. Any
suggestion?

Best regards
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.