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

[David van der Spoel]

Yinghong wrote:
> David:
>  
>  
>  > David:
>  > 
>  >  >/ 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. 舗gstr鰉?
>  > />>/ 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
>  > /
>  >  > Just realized that I repeated your calculation and got the same 
> result.
>  >  > How about exclusions? Have you checked the tpr file for that?
>  > 
>  > Firstly, thanks for your calculating in person. Which result did you
>  > get, 0.1nm or 0.01nm?
>  >See above.
>  
>  > 
>  > In my simulation, I did not define the exclusions in top file. Instead,
>  > I defined two energy groups in mdp file: SHELL & Others. Here, I
>  > wanna check whether the movement of shell particle is only related to
>  > external field in the absence of any other non-bonded interations
>  > between shell and other atoms. So, I defined "energygrp_excl = SHELL 
>  > Others" in mdp files. Is that right?
>  >Maybe, but I'm not sure.
>  
> 
>  > 
>  > Besides, I checked the tpr file, which seems ok.
>  >Does this mean that all exclusions were there?
>  >Is there interaction energy between shell and others in the output edr 
> file?
>  
> Some other information should be useful for your help. Actually, I have 
> succeeded in defining such a shell model previously. In those 
> simulations, I set polarizability alpha = 0.05 nm^3,  qS = 0.6e and mSH 
> = 10 a.u., from which the movement of shell particles are linearly 
> proportional to the external field and agree with theoretical result. 
> But, When I change the values of alpha and qS to the current case (alpha 
> = 0.3 nm^3, and qS = 3e), I can not get a satisfied result any more. Do 
> you have any suggestion to this point?
no, but try running an energy minimization and check the final coordinates.


>  
>  
> Thanks again.
>  
>  
> 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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