[gmx-users] Dipole moment

[Javier Cerezo]

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