[gmx-users] ambar to opls force field
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Mon May 9 04:23:00 CEST 2011
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)
When I use half Kbond value I get proper dielectic constant for water
(~80). I checked the Kbond for OH in opls force field is around ~ 440000.
I don't now where I am going wrong.
Here I pasted spc_fw.itp file
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
;1 3 yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_1001 OW 8 15.99940 -0.820 A 3.1655e-01 6.503e-01
opls_1002 HW 1 1.00800 0.410 A 0.00e+00 0.00e+00
[ 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
[ moleculetype ]
; Name nrexcl
WAT 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 opls_1001 1 WAT OW 1 -0.82 15.99940 ;
2 opls_1002 1 WAT HW1 1 0.41 1.008 ;
3 opls_1002 1 WAT HW2 1 0.41 1.008 ;
[ bonds ]
; i j funct
1 2 1
1 3 1
[ angles ]
; i j k funct
2 1 3 1
In water.top file, I included spc_fw.itp file.
; Include water topology
#include "spc_fw.itp"
Is there any thing worng in .itp file or where I am making mistake.
Thanks
Nilesh
On Sun, May 8, 2011 10:55 am, Justin A. Lemkul wrote:
>
>
> 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
>>>
>>>
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
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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
>
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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