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#10412 04/28/06 06:16 AM
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Hi, all users!

I want to calculate the dipole moment of water which I used as a solvent for my system. There is a command to do that, "coor dipole", but I don't know whose dipole moment that command calculates. After doing that, I got three magnitudes for three components and one total magnitude, but I don't think that they are for water only.
So, is there any method to calculate the dipole moment of water only?
Thanking you in anticipation.


Han, Jaebeom Department of Chemistry and Center for Multidimensional Spectroscopy Korea University, Seoul 136-713 Korea
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From corman.doc: " Calculates the dipole moment of selected atoms."


Lennart Nilsson
Karolinska Institutet
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Thank you, Dr. Nilsson
I could get the values of dipole moments.
However, they were vector-summed values for all coordinates which I wrote in my trajectory file.
So, can I calculate dipole moment for each water molecule per 10 steps when I wrote coordinate in my trajectory file during the simulation?


Han, Jaebeom Department of Chemistry and Center for Multidimensional Spectroscopy Korea University, Seoul 136-713 Korea
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rmv Offline
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The TIP3P (or TIP4P) water molecule is rigid with fixed charges; the dipole of a single water molecule is therefore unchanging.


Rick Venable
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I also simulated my system with TIP4P-FQ. In the case of TIP3P, I got the values similar to the reference (William L. Jorgensen et al. J. Chem. Phys. 79, 926 (1983)), but in the case of TIP4P-FQ, they are all underestimated than the value from the paper by Steven W. Rick et al. (J. Chem. Phys. 101, 6141 (1994))
So, I want to calculate the dipole moment of water with regard to time.


Han, Jaebeom Department of Chemistry and Center for Multidimensional Spectroscopy Korea University, Seoul 136-713 Korea
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rmv Offline
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The dipole moment commands (COOR DIPOLE, or DIPOLE time series in CORREL) allow atom selections; use that feature to calculate a dipole moment for an individual TIP4P-FQ water molecule. If you have 500 water molecules, then you need to declare 500 time series ...

For the dipole moment, you should get Jorgensen's value exactly for TIP3P (rigid, fixed charge); if not, you may have made a mistake, such as omitting the SHAKE command. The dipole moment of TIP3P water should be a fixed constant.


Rick Venable
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If I want to calculate average dipole of water molecules of each frame, how to loop over every molecule in the system?

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rmv Offline
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If the model was built carefully and the RESIDs are sequential (this is not guaranteed, you should check) you can just loop over the RESID numbers of the water segment.


Rick Venable
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To obtain the average over all water molecule, a slightly more straightforward approach is to directly compute the total dipole of the waters in each frame (corman.doc):
COOR DIPO SELE RESN TIP3 END
Then divide by the number of water molecules (?NSEL) to get the average.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  BRBrooks, lennart, rmv 

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