[gmx-users] Definition of "polarization"

David van der Spoel spoel at xray.bmc.uu.se
Wed Dec 14 18:52:19 CET 2005

Yinghong 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.
gmxdump -s topol.tpr | less
search for POL

> Waiting for your response, any instruction will be greatly appreciated.
> Xie Yinghong
> Hong Kong Univ.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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