[gmx-users] ambar to opls force field

[Justin A. Lemkul]

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

========================================