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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: Tue, 9 Dec 2014 18:18:48 -0500 (EST)

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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