Nilesh Dhumal wrote:
Hello Justin,
In the J. Chem. Phys. paper author have run the simulation 6.5 ns. So
I run the simulation 6.5 ns for collecting data and I have total 256 water
molecules.
I also asked how you calculated the dielectric constant.
When trying to replicate others' work, it is often most beneficial and less
time-consuming to simply contact the corresponding author of the paper. They
can talk with you directly about methodological details.
-Justin
NIlesh
On Sun, May 8, 2011 11:58 pm, Justin A. Lemkul wrote:
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
--
========================================
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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========================================
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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