[gmx-users] ambar to opls force field

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello Justin,
> 
> Here I have done some analysis.  The original value reported in J.Chem.
> Phys. 124, 024503 2006, paper are
> Kbond = 443153.3808 kJ/mol nm**2
> Kangle = 317.5656 kJ/mol rad**2.
> 
> 
> Below are the results for the dielectric constant of water.I made the .itp
> file  pasted below the table. Bond length is nm.
> 
> bond length  Kbond         angle    Kangle    dielectric constant
> 0.1012       443153.3808    113.24  317.5656       ~1.9 : orginal value
> 
> 0.1012       221576.6904    113.24  317.5656       ~80   : 1/2 (Kbond)
> 
> 0.1012       443153.3808    113.24  158.7828       ~1.58 : 1/2 (kangle)
> 
> 0.1012      221576.6904    113.24  317.5656       ~1.9   : 1/2
> (Kbond)&(Kangle)
> 

How were these dielectric constants calculated?  Did you collect sufficient 
data?  It seems to me that there is no definitive dependence on any of these 
parameters, and you have one outlying point that is coincidentally close to what 
you want.  A consistently wrong dielectric would suggest that either you're not 
calculating it right or you don't have sufficiently converged data.

Based on a quick look through the paper, it seems to me that your original 
premise of converting between force fields is not related to the task at hand. 
Water models are relatively force field-agnostic, especially when trivial 
functional forms, such as harmonic potentials, are applied.  There is nothing 
fancy here.

Given the following:

> [ bondtypes ]
> ; i    j  func       b0          kb
>   OW    HW      1    0.1012   443153.3808   ; J. Chem. Phys.
> (2006),124,024503
> [ angletypes ]
> ;  i    j    k  func       th0       cth
>   HW     OW     HW      1   113.24  158.7828 ; J. Chem. Phys.
> (2006),124,024503
> 

You are indeed applying simple harmonic potentials (see the manual to confirm 
the form), which again indicates to me that you should not be playing with the 
force constants in the model described in the paper.  Use Ka and Kb as listed. 
Halving these quantities will result in a harmonic potential, e.g. for bonds of 
(1/4)Kb(b-b0)^2 rather then the proper coefficient of 1/2.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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