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From: |
Steve Plimpton <sjplimp@...24...> |

Date: |
Wed, 10 Dec 2014 06:00:40 -0700 |

>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)).

>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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**Follow-Ups**:**Re: [lammps-users] dihedral_style/opls parameters for lammps***From:*gilbert@...3803...

**Re: [lammps-users] dihedral_style/opls parameters for lammps***From:*Axel Kohlmeyer <akohlmey@...24...>

**References**:**[lammps-users] dihedral_style/opls parameters for lammps***From:*conor parks <coparks2012@...24...>

**Re: [lammps-users] dihedral_style/opls parameters for lammps***From:*Andrew Jewett <jewett.aij@...24...>

**Re: [lammps-users] dihedral_style/opls parameters for lammps***From:*conor parks <coparks2012@...24...>

**Re: [lammps-users] dihedral_style/opls parameters for lammps***From:*gilbert@...3803...

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