[gmx-users] ambar to opls force field

[Justin A. Lemkul]

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

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