[gmx-users] dipole moment

[David van der Spoel]

On 2011-05-25 20.42, Nilesh Dhumal wrote:
> 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.
>
Of course.
How about g_velacc
> 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
>>>>>> 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
>>>> http://lists.gromacs.org/mailman/listinfo/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 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