[gmx-users] OPLSAA parameters
Elisabeth
katesedate at gmail.com
Mon Aug 1 02:25:18 CEST 2011
Hi Justin,
So far I have been #including ffoplsaa.itp and running simulations. The
reason I was after parameters is just to have a better indea on the FF
parameters rather than just using them blindly, that's it :)
Thank you,
On 31 July 2011 20:03, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Elisabeth wrote:
>
>> Thanks Justin for your guidance. By following your tips, I have now all
>> the parameters I need... Please let me know if I am missing any [ angletypes
>> ] or [ dihedraltypes ] for a hydrocarbon molecule.
>>
>>
> Seems fine to me; grompp will complain if something is missing. Is there a
> reason that you're trying to parse out certain parameters? It'd be far
> easier to just #include "oplsaa.ff/forcefield.itp" in your topology and have
> the entire OPLS-AA force field available to you, rather than reinventing the
> wheel.
>
> -Justin
>
> Best,
>>
>> [ bondtypes ]
>> ; i j func b0 kb
>> CT CT 1 0.15290 224262.4 ; CHARMM 22 parameter file
>> CT HC 1 0.10900 284512.0 ; CHARMM 22 parameter file
>>
>> [ angletypes ]
>> ;i j k func th0 cth
>> CT CT CT 1 112.700 488.273 ; CHARMM 22 parameter file
>> CT CT HC 1 110.700 313.800 ; CHARMM 22 parameter file
>> HC CT HC 1 107.800 276.144 ; CHARMM 22 parameter file
>>
>> [ dihedraltypes ]
>> CT CT CT CT 3 2.92880 -1.46440 0.20920 -1.67360
>> 0.00000 0.00000 ; hydrocarbon all-atom
>> CT CT CT HC 3 0.62760 1.88280 0.00000 -2.51040
>> 0.00000 0.00000 ; hydrocarbon all-atom
>> HC CT CT HC 3 0.62760 1.88280 0.00000 -2.51040
>> 0.00000 0.00000 ; hydrocarbon *new* 11/99
>>
>>
>>
>>
>>
>> On 30 July 2011 07:40, Justin A. Lemkul <jalemkul at vt.edu <mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> Elisabeth wrote:
>>
>> Hello to all,
>>
>> I am looking for bonded and nonbonded parameters for C H atoms
>> in saturated hydrocarbons.
>>
>> atom types are:
>> Carbon atoms opls_135 opls_136 H opls_140
>> opls_135 12.01100 ; alkane CH3
>> opls_136 12.01100 ; alkane CH2
>> opls_140 1.00800 ; alkane H.
>>
>> Please help me out with the following:
>>
>> - I am wondering if I am selecting the correct values, for C-C
>> and C-H bonds from ffoplsaabon.itp.
>>
>>
>> The C-C bond is not correct for alkanes. It is for the C-C bond of
>> oxalic acid, as the comment indicates. In ffnonbonded.itp, you can
>> see how opls_* types are mapped to different bonded atom types (for
>> instance, opls_135/136 are CT). Note that in the topology, you do
>> not have to explicitly define values when using OPLS-AA; any bond
>> between two defined bonded atom types will be automatically detected
>> and used.
>>
>>
>> C C 1 0.15100 292880.0 ; wlj oxalic acid, etc.
>> HC C 1 0.10900 284512.0 ; wlj 7/96
>>
>> - what does wlj mean?
>>
>>
>> Probably someone's initials, which occur frequently to indicate
>> either the source of the parameters or the individual that added
>> them. In this case, my guess would be Jorgensen is the referenced
>> individual here.
>>
>> - what are the units?
>>
>>
>> This is in the manual.
>>
>>
>>
>> Angle
>>
>> CA CA CZ 1 120.000 585.760 ; wlj
>> CA CA CR 1 120.000 527.184 ;
>> CA CA CX 1 120.000 711.280 ;
>> C CT Cl 1 109.800 577.392 ; wlj
>>
>> - I can not distinguish CA CZ .... What are they referring to?
>>
>>
>> See the above tip about converting atom types in ffnonbonded.itp.
>>
>>
>> [ dihedraltypes ]
>>
>> C C CT HC 3 0.17782 0.53346 0.00000
>> -0.71128 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000)
>>
>> - Is this what I need for oplsaa 135 136 140?
>>
>>
>> Probably not. The comment indicates the dihedral is for
>> dicarbonyls. The appropriate dihedral is:
>>
>> CT CT CT HC 3 0.62760 1.88280 0.00000
>> -2.51040 0.00000 0.00000 ; hydrocarbon all-atom
>>
>> Note how the comment indicates it is for use with hydrocarbons.
>> Again, like bonds as described above, you do not need to explicitly
>> list parameters in the topology. They will be inferred from the
>> atom types.
>>
>>
>> ffoplsaanb.itp.
>>
>> opls_135 CT 6 12.01100 -0.180 A
>> 3.50000e-01 2.76144e-01
>> opls_136 CT 6 12.01100 -0.120 A
>> 3.50000e-01 2.76144e-01
>>
>> opls_140 HC 1 1.00800 0.060 A
>> 2.50000e-01 1.25520e-01
>>
>> - are these parameters for
>>
>> opls_135 12.01100 ; alkane CH3
>> opls_136 12.01100 ; alkane CH2
>> opls_140 1.00800 ; alkane H.
>>
>> ?
>>
>>
>> Yes.
>>
>>
>> Also in usr/local/gromacs/share/__**gromacs/top/ directory I can
>> not find ffoplsaanb,itp and ffoplsaabon.itp for 4.5.4 whereas in
>> previous versions these files were accessible. I am using itp
>> files from version 4.0.7 and wanted to make sure the above
>> parameters for oplsa_135 oplsa_136 and oplsa_140 have been
>> remained unchanged in 4.5.4. Where can I find these files?
>>
>>
>> The force field organization has changed, but the content of the
>> force fields has not. This is described in the manual. All the
>> equivalent files are now in the oplsaa.ff subdirectory. For
>> backwards compatibility, the statement #include "ffoplsaa.itp" will
>> indeed call the force field, because you will note that ffoplsaa.itp
>> now simply calls the correct force field with #include
>> "oplsaa.ff/forcefield.itp."
>>
>> -Justin
>>
>> -- ==============================**__==========
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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