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Re: [lammps-users] dihedral_style/opls parameters for lammps
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Re: [lammps-users] dihedral_style/opls parameters for lammps


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 10 Dec 2014 16:27:45 -0500

On Wed, Dec 10, 2014 at 4:23 PM, conor parks <coparks2012@...24...> wrote:
> Thank you so much for pointing out that tutorial. I had skimmed it
> previously, but missed the link to the input script. Just for clarification
> for ethane, the H is type 46 and the C is type 13 I believe. The torsion
> angle listed in the oplsaa.prm file is
>
> torsion 46 13 13 46  0.000 0.0 1  0.000 180.0 2  0.300 0.0 3
>
> What am I missing for the choice of the 0.318 value for the K3?

that you should ask the tinker folks. i looked up the parameters in
the referenced publication.

axel.

>
> conor
>
> On Wed, Dec 10, 2014 at 8:04 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>> On Wed, Dec 10, 2014 at 8:00 AM, Steve Plimpton <sjplimp@...24...> wrote:
>> >>The lammps documentation for dihedral_style opls is correct for the
>> >>equations but the numeric example is total nonsense and worse than
>> >>useless. The values listed of 1 90.0 90.0 90.0 would give 6*90 kcal of
>> >>torsional energy for the V2 term in a normal single bond. A normal
>> >> sp3-sp3
>> >>single bond has six torsions and each one would contribute
>> >>90*(1+cos2(phi)).
>> >
>> > Please suggest a good example for the doc page and we'll replace it.
>> > I don't use OPLS.
>>
>> here are the numbers for the hydrocarbon inputs in the topotools
>> tutorial (in real units):
>>
>> dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT
>> dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC
>> dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC
>>
>>
>> >
>> > Steve
>> >
>> > On Tue, Dec 9, 2014 at 4:18 PM, <gilbert@...3803...> wrote:
>> >>
>> >> You should see the tutorial on Axel Kohlmeyer's home page where he does
>> >> several small hydrocarbons using OPLSAA:
>> >>
>> >>
>> >>
>> >> https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2
>> >>
>> >> You can see the parameters he uses (in.step2b and in.step2e_2) are
>> >> identical to 1-1-1-1 parameters in the oplsaal.prm file that comes with
>> >> Tinker5.
>> >>
>> >> The lammps documentation for dihedral_style opls is correct for the
>> >> equations but the numeric example is total nonsense and worse than
>> >> useless. The values listed of 1 90.0 90.0 90.0 would give 6*90 kcal of
>> >> torsional energy for the V2 term in a normal single bond. A normal
>> >> sp3-sp3
>> >> single bond has six torsions and each one would contribute
>> >> 90*(1+cos2(phi)).
>> >>
>> >> kevin
>> >>
>> >> > Thank you so much for that thorough response. I apologize for
>> >> > bringing a
>> >> > tinker question to the lammps email list. I honestly thought lammps
>> >> > was
>> >> > doing something different because of that mysterious V4. Specifically
>> >> > about
>> >> > lammps, the dihedral_opls function I am looking at is (
>> >> > http://lammps.sandia.gov/doc/dihedral_opls.html):
>> >> >
>> >> > 0.5*k1*(1+cosx) + 0.5*k2*(1-cos2x)+0.5*k3*(1+cos3x)+0.5*k4*(1-cos4x)
>> >> >
>> >> > The second and fourth term in the user manual already has the sign
>> >> > flipped,
>> >> > unlike the one you wrote. How would this still affect the sign flip
>> >> > you
>> >> > mentioned by the 180 degrees f2?
>> >> >
>> >> > conor
>> >> >
>> >> > On Fri, Dec 5, 2014 at 4:55 PM, Andrew Jewett <jewett.aij@...24...>
>> >> > wrote:
>> >> >
>> >> >> On Fri, Dec 5, 2014 at 11:24 AM, conor parks <coparks2012@...24...>
>> >> >> wrote:
>> >> >> > I have been having a hard time figuring out where to get  the OPLS
>> >> >> dihedral
>> >> >> > parameters for lammps. I see in the OPLS dihedral form used by
>> >> >> > lammps,
>> >> >> one
>> >> >> > specifies the V1 V2 V3 and V4 in the dihedral_coeff command.
>> >> >> > However,
>> >> >> in
>> >> >> all
>> >> >> > the OPLS parameter sets I have looked at, the one given in tinker
>> >> >> being
>> >> >> what
>> >> >> > I think is close to the latest version of OPLS
>> >> >> > (http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm), I
>> >> >> > only
>> >> >> see a
>> >> >> > mention of what I believe to be V1 V2 V3 and f1 f2 f3 where the
>> >> >> > latter
>> >> >> are
>> >> >> > the phase angle offsets.
>> >> >> ...
>> >> >> > or is there some
>> >> >> > conversion between the V1 V2 V3 f1 f2 f3 to the V1 V2 V3 V4 sets
>> >> >> > that
>> >> >> I
>> >> >> am
>> >> >> > missing.
>> >> >>
>> >> >>
>> >> >> You are asking for details about the format of the "oplsaa.prm"
>> >> >> file,
>> >> >> which is is not part of LAMMPS.  It is a file distributed with the
>> >> >> TINKER software, and used by MOLTEMPLATE.
>> >> >> Since I wrote moltemplate, I will do my best to answer.
>> >> >> If you discover that my answer is incorrect, please let me know.
>> >> >>
>> >> >> However, this file is distributed by the Ponder lab, and they are
>> >> >> the
>> >> >> authoritative source for information about this file.
>> >> >>
>> >> >> Anyway, in the 2001 JPCA paper cited by the LAMMPS manual,
>> >> >> (
>> >> >>
>> >> >>
>> >> >> http://courses.chem.psu.edu/chem408/reading/MM_topics/jorgensen_perfluoro_jpca_2001.pdf
>> >> >> )
>> >> >> the formula for the torsion energy is:
>> >> >>
>> >> >> 0.5*(V1*(1+cos(x+f1) + V2*(1-cos(2x+f2)) + V3*(1+cos(3x+f3)) +
>> >> >> V4*(1-cos(4x+f4)))
>> >> >>
>> >> >> There is no general way to convert this formula to the formula used
>> >> >> by
>> >> >> LAMMPS' "dihedral_style opls", for arbitrary values of f1,f2,f3,f4
>> >> >>
>> >> >> http://lammps.sandia.gov/doc/dihedral_opls.html
>> >> >>
>> >> >> For dihedral style opls, the energy is:
>> >> >> 0.5*(K1*(1+cos(x)) + K2*(1+cos(2x)) + K3*(1+cos(3x)) +
>> >> >> K4*(1+cos(4x)))
>> >> >>
>> >> >> (Note there is a sign change in the two formulas.: "1-cos(2x+f2)"
>> >> >> instead of   "1+cos(2x)".)
>> >> >>
>> >> >> However, it turns out that, for every torsion interaction in OPLSAA:
>> >> >> f1=0
>> >> >> f2=180   # (this negates the sign change)
>> >> >> f3=0
>> >> >> f4=180
>> >> >> (See the torsion section of that "oplsaa.prm" file.)  Consequently,
>> >> >> the "dihedral_style_opls" formula is general enough, and the
>> >> >> conversion you are looking for is:
>> >> >>
>> >> >> K1 = V1
>> >> >> K2 = V2
>> >> >> K3 = V3
>> >> >> K4 = V4
>> >> >>
>> >> >> (This is what Jason Lambert's "oplsaa_moltemplate.py" script does
>> >> >> when
>> >> >> it converts the "oplsaa.prm" file into moltemplate format
>> >> >> (oplsaa.lt).)
>> >> >>
>> >> >>
>> >> >> > Finally, I am having a hard time interpreting the parameters in
>> >> >> > the
>> >> >> torsional part of
>> >> >> > the oplsaa file. For instance,
>> >> >> >
>> >> >> > torsion      13    3   20   13      4.669 0.0 1   5.124 180.0 2
>> >> >> 0.000
>> >> >> 0.0 3
>> >> >> >
>> >> >> > I am assuming 4.669,5.124,and 0.000 correspond to a V1 V2 V3. Is
>> >> >> > this
>> >> >> true?
>> >> >>
>> >> >> Yes.
>> >> >>
>> >> >> > What are the 1 2 3 referring to along with the 0.0 180.0 0.0 (I am
>> >> >> assuming these are a f1,f2,f3).
>> >> >>
>> >> >> Yes.
>> >> >>
>> >> >> (The "1", "2" and "3", are the integer frequencies in the Fourier
>> >> >> expansion.  They never vary in the "oplsaa.prm" file.  They are
>> >> >> always
>> >> >> 1,2,3.)
>> >> >>
>> >> >> Unfortunately, the "oplsaa.prm" file does not include V4 parameters.
>> >> >> However, they are not needed if you are using the original, basic
>> >> >> OPLSAA force-field.  In that case V4=0.  (Apparently V4 is non-zero
>> >> >> for the perfluouroalkanes discussed in the 2001 paper, but not in
>> >> >> the
>> >> >> original 1996 OPLSAA paper.  See below.)
>> >> >>
>> >> >> > The Watkins paper cited in the lammps manual only
>> >> >> > provides parameters for perfluouroalkanes, so I was wondering
>> >> >> > where I
>> >> >> need
>> >> >> > to go to obtain these parameters for other molecules,
>> >> >>
>> >> >> The original OPLS paper is from 1996, and it is not only for
>> >> >> perfluouroalkanes
>> >> >> http://pubs.acs.org/doi/abs/10.1021/ja9621760
>> >> >>
>> >> >> It uses the same formula for the dihedral energy.
>> >> >>
>> >> >> Incidentally, you do not have to use "dihedral_style opls" to
>> >> >> simulate
>> >> >> molecules using the OPLS force-fields in LAMMPS.  If you want a more
>> >> >> general formula, I recommend "dihedral_style fourier".
>> >> >> http://lammps.sandia.gov/doc/dihedral_fourier.html
>> >> >> That dihedral style will allow you to customize the f1,f2,f3,f4,...
>> >> >> offsets, and the frequencies as well (1,2,3,4,...)
>> >> >>
>> >> >> If you need more detail than this, the TINKER mailing list is
>> >> >> probably
>> >> >> the best source of information.
>> >> >>
>> >> >> Andrew
>> >> >>
>> >> >
>> >> >
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>> >>
>> >>
>> >>
>> >>
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>>
>>
>> --
>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>



-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.