[gmx-users] ambar to opls force field

[Nilesh Dhumal]

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.
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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