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

Yinghong xieyh at hkusua.hku.hk
Tue Dec 20 06:59:59 CET 2005


> 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?

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?

Besides, I checked the tpr file, which seems ok. 

Xie Yinghong
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