[gmx-users] Dipole moment

[Nilesh Dhumal]

Is it possible to calcualte the dipole moment at 3fs by modifing the
source code?

Nilesh


> How can I save the total dipole moment extacted by .edr file?
>
> I could not find the option in g_energy.
>
> Nilesh
>
>
>> Justin is right. I've slipped a bit, that was not the way to set
>> nstenergy. But still, you can save the dipole directly in the edr file.
>> Not from your existing trajectory, but in a new run. Say your dt=1fs,
>> then you should set nstenergy=3 to get your dipole moment every 3fs
>> which you can retrieve with g_energy.
>>
>> Javier
>>
>>
>> El 18/10/12 20:43, Nilesh Dhumal escribió:
>>> In short, I can not save dipole moment directly. I can calculate dipole
>>> moment only using .trr file.
>>>
>>> Nilesh
>>>> On 10/18/12 1:45 PM, Javier Cerezo wrote:
>>>>> Hi
>>>>>
>>>>> The dipole is stored in the edr file, which output frequency is
>>>>> controlled by
>>>>> "nstenergy" option in the mdp parameter file. Set it appropriately
>>>>> during your
>>>>> run (nstenergy=0.003) but keep in mind that it should be a multiple
>>>>> of
>>>>> the time
>>>>> step.
>>>>>
>>>> nstenergy cannot be set this way; it is an integer indicating the
>>>> interval
>>>> (in
>>>> number of steps) for writing energy values.  If the values have been
>>>> saved
>>>> every
>>>> 2 ps, there is no way to retrieve them every 3 fs; if more frequent
>>>> information
>>>> is needed, it needs to be saved more frequently.
>>>>
>>>> -Justin
>>>>
>>>>> El 18/10/12 18:09, Nilesh Dhumal escribió:
>>>>>> Hello,
>>>>>>
>>>>>> I am calculating the dipole moment auto-correlation function for my
>>>>>> system
>>>>>> which have 128 cation and 128 anion.
>>>>>>
>>>>>> I am saving the trajectory at each 2 ps and using this trajectory
>>>>>> for
>>>>>> further analysis.
>>>>>>
>>>>>> Can I save the dipole moment and three vectors at each 3 fs?
>>>>>>
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Nilesh
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Research Scientist
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
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>>>
>>
>> --
>> Javier CEREZO BASTIDA
>> Ph.D. Student
>> Physical Chemistry
>> Universidad de Murcia
>> 30100, Murcia (SPAIN)
>> T: (0034)868887434
>>
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