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

[Yinghong]

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. 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
> /
>  > 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?

I can not completely understand the meaning of exclusions in tpr file. But, I found some information about "energygrp_excl" in tpr file, instead.
For example, I defined four energy groups in my system: SOL  Benzene  SHELL  DUMMY. 
Then, the following stuff was what I located in tpr file.
      energygrp_excl[  0]: 0 0 1 0
      energygrp_excl[  1]: 0 0 1 0
      energygrp_excl[  2]: 1 1 1 0
      energygrp_excl[  3]: 0 0 0 0
Which should mean I have excluded the interactions between SHELL and the other three groups. So, I think that is no problem to this point.
Besides, I read the edr file, which also told me the non-bonded interactions between SHELL and other groups were all equal to zero.

By the way, on the temperature coupling, I set the temperature as the follows:
Tcoupl              =  berendsen
tc-grps             =  SOL  Benzene   SHELL    DUMMY  
tau_t               =    0.1        0.1         0.001         0.1 
ref_t               =    300       300           10           300

As I think, 10K of temperature of SHELL will not influence the magnitude of shell movement from the viewpoint of hydrodynamics. Because a high temperature (e.g. 300K) will greatly enhance the kinetics of shell particles, which possibly made shell particle very active and beyond the control of such a weak spring with Kr = 4100 KJ/mol/nm^2, as well as finally led to the interrupt of simulation. So, what is your consideration about this point?

Also, I give a mass of 10.0 a.u. to shell particles. As I observed, so large a mass will not also influence the magnitude of shell movement, instead, it is only for decreasing the fluctuation of shell particles. Any doubt?

Thanks.


Xie Yinghong
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