LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] dihedral_style/opls parameters for lammps
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 10 Dec 2014 08:04:05 -0500

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
>> >>
>> >
>> > ------------------------------------------------------------------------------
>> > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
>> > from Actuate! Instantly Supercharge Your Business Reports and Dashboards
>> > with Interactivity, Sharing, Native Excel Exports, App Integration &
>> > more
>> > Get technology previously reserved for billion-dollar corporations, FREE
>> >
>> > http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk_______________________________________________
>> > lammps-users mailing list
>> > lammps-users@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/lammps-users
>> >
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
>> with Interactivity, Sharing, Native Excel Exports, App Integration & more
>> Get technology previously reserved for billion-dollar corporations, FREE
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
>> _______________________________________________
>> lammps-users mailing list
>> lammps-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
> _______________________________________________
> lammps-users mailing list
> lammps-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>



-- 
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.