[gmx-users] Dipole moment

[Nilesh Dhumal]

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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