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

[David van der Spoel]

Yinghong wrote:
> David:
> 
>  >/ 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?
> I am very sure it is not that problem. Upon the parameters mentioned 
> above, rsd should be ~0.1nm theoretically, but my calculation gave a 
> value of only 0.01nm. So, any other suggestion?
>  
>  

We have

F = q E = k r or
r = q E / k
r = 0.00108 (eV/kj/mol) nm
   = 0.1 nm



> Thanks
>  
>  
> Xie Yinghong
> 
> 
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-- 
David.
________________________________________________________________________
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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