[gmx-users] Definition of "polarization"

Yinghong xieyh at hkusua.hku.hk
Thu Dec 15 02:57:45 CET 2005

Dear Gmx'ers:

As mentioned in the publication about shell water model, a shell particle is connected to a dummy atom by a spring-like connection with the following relationship:

1. K=sqr(qS)/(4*PHI*Epsilon*alpha), 
2. rsd=(4*PHI*Epsilon*alpha)*E / qS;  (rsd is the distance between shell and dummy particles at any moment, and E is refered to electrical field strength).

Anyone can tell me where is the definition of two equations above, especially in the case of "isotropic polarization", in GMX source code.
Because in my simulation, what I want to polarized is not a water molecule. So I need a definite instruction, any suggestion?

Secondly, how can I read the calculated value of spring constant K by GMX after I defined "alpha" and "qS"? Can "debug" realize it? If yes, how? Although I have used GMX for a long time, but that is the first time for me to encounter such a problem.

Waiting for your response, any instruction will be greatly appreciated.

Xie Yinghong
Hong Kong Univ.
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