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: conor parks <coparks2012@...24...>
Date: Fri, 5 Dec 2014 17:12:01 -0500

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@...36.....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