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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 >> > ------------------------------------------------------------------------------ > 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 >

**Follow-Ups**:**Re: [lammps-users] dihedral_style/opls parameters for lammps***From:*Steve Plimpton <sjplimp@...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...>

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