[gmx-users] ambar to opls force field
Justin A. Lemkul
jalemkul at vt.edu
Mon May 9 05:58:20 CEST 2011
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
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
Given the following:
> [ bondtypes ]
> ; i j func b0 kb
> OW HW 1 0.1012 443153.3808 ; J. Chem. Phys.
> [ angletypes ]
> ; i j k func th0 cth
> HW OW HW 1 113.24 158.7828 ; J. Chem. Phys.
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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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