Nilesh Dhumal wrote:
Thanks Justin.
I am using flexibale water model for my system. I am refering a paper J.
Chem. Phys. 124, 024503 (2006). Author have used Amber type force field.
i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2.
Kbond = 443153.3808 kJ/mol nm**2
Kangle= 317.5656 kJ/mol rad**2.
I am using olss-aa force field parameters in Gromacs VERSION 4.0.7.
I checked some papers in which author have used opls aa force field. 1/2
factor is not in opls force field IF I compare opls and amber.
My question is in .itp file should I use Kbond and Kangle as it is or
should I consider the 1/2 factor then I use them.
Both of those terms are simple harmonic expressions, which do not require any
modification. Per the manual, Gromacs uses these expressions as is, so Kb and
Ka should be appropriate as listed. They are of comparable magnitude to
existing bonded parameters for such terms.
You can, of course, test this by using the same parameters under the original
AMBER force field used in the paper you cite, and then again after incorporation
into the OPLS-AA force field. If the resulting averages are the same, then the
new parameters have been incorporated correctly.
-Justin
Thanks
Nilesh
On Fri, May 6, 2011 6:36 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
How can I convert ambar force field to opls force field.
Should I half the force constant of bond (Ka) and angle (Kb)?
Why would you do that? Most of the bonded parameters in OPLS were taken
from AMBER directly, IIRC. If you need to parameterize some new bonded
parameters, you'd be better served deriving them in a way that is
compatible with the modern OPLS-AA force field (probably QM/geometry
optimization), rather than trying to hack something together.
-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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