[gmx-users] Dipole moment

[Javier Cerezo]

When calculated during the md run, the corresponding options in g_energy 
for the dipole moment are MU-X, MU-Y and MU-Z.

However, taking into account the previous mail by David van der Spoel, 
it's possible that the dipole moment could not be calculated in your 
system. Options in g_energy vary depending on the actual computation.

If you want to calculate the dipole moment by your own, I think it's 
easier to use the xtc file exported every 3fs (it'll be considerably 
heavier than the edr file, however) and writing an specific code for 
your purposes. In order to read the trajectories, you can use the xtc 
library 
(http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library). 
Anyway, if the code didn't compute it, there should be a reason.

Javier


El 19/10/12 04:42, Nilesh Dhumal escribió:
> 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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>

-- 
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434