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I want to determine the potential energy of two equally charged spherical charges by using the equation: $V_{pot}= \int_V \frac{1}{2} \epsilon_0 E^2 dV$ and therefore I was wondering what I has to take as $E$? The sum of the electric fields of both charges? Notice, that I want to use this equation on purpose since it enables me to determine the potential energy in a particular volume.

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Yes it's the total field. – Michael Brown Jul 25 '13 at 9:24
Are the two spheres conductors? Isolators? (Things are getting complicated if spheres are conductors.) – Sawi Jul 25 '13 at 11:23
They are conductors, what would be the equation then? – Xin Wang Jul 25 '13 at 11:24
Well, it's quite complicated (excuse: I'm not in the mood to do that) because the distribution of charges in both spheres are no longer uniform. – Sawi Jul 25 '13 at 11:27
Scratching quickly on a piece of paper, I think that there are no exact closed-form expression for $E$. (I can be wrong) – Sawi Jul 25 '13 at 12:32

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