[gmx-users] dipole moment

[David van der Spoel]

On 2011-05-25 18.03, Nilesh Dhumal wrote:
> Thanks for reply.
>
> Here are more details about my simulation.
>
> I have glucose molecule in my system. I am interested in change in dipole
> moment of OH bond of glucose along the simulation.

The OH group is not neutral so your dipole is meaningless (position 
dependent).

Otherwise the charges are constant and the fluctuation in bond length 
(if you have a flexible molecule) will be small, or zero with 
constraints. You should think what you want to get out. What experiment 
you want to compare to.
>
> I have made the index file.
>
> How can I select two groups (oxygen and hydrogen) or should I put
> particular oxygen and hydrogen in same group (manually).
>
> Nilesh
>
> On Wed, May 25, 2011 11:59 am, David van der Spoel wrote:
>> On 2011-05-25 17.36, Nilesh Dhumal wrote:
>>
>>> I want to see the change in dipole moment alond the simulation.
>>>
>> g_dipoles -h
>>
>>>
>>>
>>> NIlesh
>>>
>>>
>>> On Wed, May 25, 2011 11:32 am, David van der Spoel wrote:
>>>
>>>> On 2011-05-25 17.14, Nilesh Dhumal wrote:
>>>>
>>>>
>>>>> Hello,
>>>>>
>>>>>
>>>>>
>>>>> Can I calculate a dipole moment of a particular bond?
>>>>>
>>>>>
>>>> It is easier to do it manually. Otherwise g_dipoles with a suitable
>>>> index file would do it. The sum of charges has to be zero of course.
>>>>>
>>>>> I am using gromacs version 4.0.7.
>>>>>
>>>>>
>>>>>
>>>>> Thanks
>>>>>
>>>>>
>>>>>
>>>>> Nilesh
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Dept. of Cell&   Molec. Biol., Uppsala University.
>>>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se -- gmx-users mailing
>>>> list    gmx-users at gromacs.org
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>>>>
>>>>
>>>
>>>
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell&  Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se --
>> gmx-users mailing list    gmx-users at gromacs.org
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>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se