[gmx-users] Definition of "polarization"

Omololu Akin-Ojo prayerz4users at yahoo.com
Wed Dec 14 23:37:21 CET 2005

 take a look at the sw.itp file in share/top in your gromacs installation directory. it is an example for water. You could modify it for your use. there are useful comments in it too.

Yinghong <xieyh at hkusua.hku.hk> wrote:     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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