[gmx-users] ambar to opls force field
Justin A. Lemkul
jalemkul at vt.edu
Mon May 9 17:12:55 CEST 2011
Nilesh Dhumal wrote:
> 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.
>
The manual and the archive are not clear on the proper way to calculate a
dielectric constant, but it seems your use of g_dipoles neglects several terms
that may affect your outcome. I would suggest backing up and applying your
methodology to a well-defined system like rigid SPC to see if you can recover
the proper dielectric constant for that system (65, I believe). That will tell
you if your method for calculating the dielectric is correct. If it is, and you
still can't reproduce the results for the flexible model, my advice is still to
contact the authors of the cited paper for advice.
-Justin
>
> 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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>
>
>
--
========================================
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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