[gmx-users] ambar to opls force field

[Nilesh Dhumal]

I used g_dipoles to calculate dielectric constant.


g_dipoles -f water.trr -s water.tpr -eps

Group     0 (      System) has   768 elements
Group     1 (     Protein) has   768 elements
Group     2 (   Protein-H) has   256 elements
Group     3 (     C-alpha) has     0 elements
Group     4 (    Backbone) has     0 elements
Group     5 (   MainChain) has     0 elements
Group     6 (MainChain+Cb) has     0 elements
Group     7 ( MainChain+H) has     0 elements
Group     8 (   SideChain) has   768 elements
Group     9 ( SideChain-H) has   256 elements
Select a group: 0

I selected 0.


Nilesh

On Mon, May 9, 2011 8:28 am, Justin A. Lemkul wrote:
>

>
> 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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