[gmx-users] David, doubt about the definition of polarization.

David van der Spoel spoel at xray.bmc.uu.se
Mon Dec 19 09:29:13 CET 2005

Yinghong wrote:
> Dear Dr. David:
> According to the shell water model, I used this method to another kind of molecule, which is composed of 6 atoms (e.g. benzene). Initially, I put a dummy and shell particle (a small mass is given to shell, and doing a normal dynamcis) in the center of this hexagon, in which shell particle is connected to dummy through your defined isotropic polarization method.
> Theoretically, polarization can be looked as a spring-like connection with constant Kr = sqr(qS)/4*PHI*Epsilon*Alpha, and the distance between dummy and shell particle can be decided by rsd = 4*PHI*Epsilon*Alpha * E0 / qS. Is it right?
> Now, in my simulation, I applied an external electric field along Z direction, and the interactions (vdws + coulomb) between shell particle and all the other atoms are exclued. (Of course, here, What I did is only to make a test instead of a real case). Obviously, for dummy and shell particles, E0 is currently only referred to the external field, because local field is excluded. 
> Quantitively,  I set alpha = 0.3 nm^3, qS = 3.0e and E0 = 1.5 V/nm, through "mdrun -debug", alpha and qS can be correctly output, and the calculated value for Kr = 4168 KJ/mol/nm^2 is also in the right way. After simulation, I used "g_dist" to check the distance between dummy and shell particle (rsd) under such electric field. But the calculted value for rsd is only 10 percent of the theoretical value although I have tried for many times. 
> So, Could you tell me some possible errors in my defined model, and why rsd can not approach to the theoretical value? What is the principle for GMX to calculate this rsd?

Isn't the problem nm vs. Ångström?

> Thanks.
> 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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