[gmx-users] dipole moment

[Nilesh Dhumal]

Basically I want to calculate the stretching vibration of the bond by
fourier transfrom of dipole momenet autocorrelation fucntion or velocity
autocorrelation function.

Before going for vibration I wanted to check the fluctuation of dipole
moment along the simulation.


Can I calculate the velocity autocorrelation function for a bond.

Nilesh

On Wed, May 25, 2011 12:37 pm, David van der Spoel wrote:
> 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
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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
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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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