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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: gilbert@...3803...
Date: Wed, 10 Dec 2014 18:26:47 -0500 (EST)

Axel has already provided good number for oplsaa. I looked at the other
dihederal_style commands and I think they are all not correct for the
standard organic force fields (oplsaa, mmff95, amber, charmm, mm2, mm3,
class2). All of these force fields use some variant of the sum of a series
of K*cos(n*phi), where K is the energy of the torsional barrier and
usually given in kcal. Typical examples for some of these force fields
are:

CT-CT-CT-CT  - backbone carbons in butane
          K1     K2    K3   K4
oplsaa:  1.74  -.157  .279  0
amber:     0    .18   .03   0
charmm:    0    .20   .03   0
mm3:      .185  .170  .520  0
mmff94:   .130  .681  .332  0

None of these force fields use the K4 term. You can't use the numbers
interchangeably because the 1,4 interaction depends on the vdw + charge +
torsion contributions, but the numerical values are all similar. This
applies to dihedral_styles charmm, class2, harmonic and opls. I don't know
anything about the helix style. It could be that the numeric values in the
documentation do apply to some coarse grained force fields and it would be
nice if someone would comment on this.

kevin

>>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.
>
> 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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