[gmx-users] Re: OPLS-AA force field for Benzyl alcohol and Phenylethanol
David van der Spoel
spoel at xray.bmc.uu.se
Fri Mar 18 13:13:18 CET 2011
On 2011-03-18 12.23, Cen-Feng Fu wrote:
> Hi David,
> Thanks for your suggestion. Now I have complete the topology files for
> benzyl alcohol and phenylethanol.
> However, I have a new doubt. In your topology file for benzyl alcohol,
> ; ring_180
> 1 3 5 7 1 180 4.6 2
> 3 5 7 9 1 180 4.6 2
> 5 7 9 11 1 180 4.6 2
> 7 9 11 1 1 180 4.6 2
> 9 11 1 3 1 180 4.6 2
> 11 1 3 5 1 180 4.6 2
> is this section necessary? If I don't put this section in the file, is
> the results still correct?
This is for you to find out based on the original article. There may or
may not be a reference in the atomtypes.atp. Otherwise check generic
OPLS articles.
> Thanks!
>
> > Dear Users,
> > I am trying to do some simulations for liquid benzyl alcohol and
> > phenylethanol. I want to use the OPLS-AA force field. However, I
> don't
> > know which parameters should be used for atoms in these two
> molecules.
> > In the ffnonbonded.itp file for OPLS-AA, which parameters (opls_xxx)
> > should I use. Could anyone give some suggestions? Thanks!
> Check both atomtypes.atp and the above file. Then you will be able to
> find out.
>
> I' attaching benzyl alcohol. Please double check before using it.
> >
> > --
> >
> ----------------------------------------------------------------------
> > Cen-Feng Fu
> > Department of Chemical Physics
> > University of Science and Technology of China
> > Hefei, Anhui, 230026, P.R.China
> >
> ----------------------------------------------------------------------
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> http://folding.bmc.uu.se
> -------------- next part --------------
> [ moleculetype ]
> ; Name nrexcl
> benzyl-alcohol 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 opls_145 1 LIG C 1
> -0.115 12.011
> 2 opls_146 1 LIG H 2
> 0.115 1.008
> 3 opls_145 1 LIG C 3
> -0.115 12.011
> 4 opls_146 1 LIG H 4
> 0.115 1.008
> 5 opls_145 1 LIG C 5
> -0.115 12.011
> 6 opls_146 1 LIG H 6
> 0.115 1.008
> 7 opls_145 1 LIG C 7
> -0.115 12.011
> 8 opls_146 1 LIG H 8
> 0.115 1.008
> 9 opls_145 1 LIG C 9
> -0.115 12.011
> 10 opls_146 1 LIG H 10
> 0.115 1.008
> 11 opls_221 1 LIG C 11
> -0.055 12.011
> 12 opls_218 1 LIG C 12
> 0.2 12.011
> 13 opls_140 1 LIG H 13
> 0.060 1.008
> 14 opls_140 1 LIG H 14
> 0.060 1.008
> 15 opls_154 1 LIG O 15
> -0.683 15.9994
> 16 opls_155 1 LIG H 16
> 0.418 1.008
>
> [ bonds ]
> ; ai aj funct c0 c1 c2
> c3
> 1 2 1
> 1 3 1
> 1 11 1
> 3 4 1
> 3 5 1
> 5 6 1
> 5 7 1
> 7 8 1
> 7 9 1
> 9 10 1
> 9 11 1
> 11 12 1
> 12 13 1
> 12 14 1
> 12 15 1
> 15 16 1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2
> c3
> 1 6 1
> 1 7 1
> 1 10 1
> 1 13 1
> 1 14 1
> 1 15 1
> 2 4 1
> 2 5 1
> 2 9 1
> 2 12 1
> 3 8 1
> 3 9 1
> 3 12 1
> 4 6 1
> 4 7 1
> 4 11 1
> 5 10 1
> 5 11 1
> 6 8 1
> 6 9 1
> 7 12 1
> 8 10 1
> 8 11 1
> 9 13 1
> 9 14 1
> 9 15 1
> 10 12 1
> 11 16 1
> 13 16 1
> 14 16 1
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2
> c3
> 2 1 3 1
> 2 1 11 1
> 3 1 11 1
> 1 3 4 1
> 1 3 5 1
> 4 3 5 1
> 3 5 6 1
> 3 5 7 1
> 6 5 7 1
> 5 7 8 1
> 5 7 9 1
> 8 7 9 1
> 7 9 10 1
> 7 9 11 1
> 10 9 11 1
> 1 11 9 1
> 1 11 12 1
> 9 11 12 1
> 11 12 13 1
> 11 12 14 1
> 11 12 15 1
> 13 12 14 1
> 13 12 15 1
> 14 12 15 1
> 12 15 16 1
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> 2 1 3 4 3
> 2 1 3 5 3
> 11 1 3 4 3
> 11 1 3 5 3
> 2 1 11 9 3
> 2 1 11 12 3
> 3 1 11 9 3
> 3 1 11 12 3
> 1 3 5 6 3
> 1 3 5 7 3
> 4 3 5 6 3
> 4 3 5 7 3
> 3 5 7 8 3
> 3 5 7 9 3
> 6 5 7 8 3
> 6 5 7 9 3
> 5 7 9 10 3
> 5 7 9 11 3
> 8 7 9 10 3
> 8 7 9 11 3
> 7 9 11 1 3
> 7 9 11 12 3
> 10 9 11 1 3
> 10 9 11 12 3
> 1 11 12 13 3
> 1 11 12 14 3
> 1 11 12 15 3
> 9 11 12 13 3
> 9 11 12 14 3
> 9 11 12 15 3
> 11 12 15 16 3
> 13 12 15 16 3
> 14 12 15 16 3
>
> ; added, improper
> 1 11 3 2 1 180 4.6 2
> 3 1 5 4 1 180 4.6 2
> 5 3 7 6 1 180 4.6 2
> 7 5 9 8 1 180 4.6 2
> 9 7 11 10 1 180 4.6 2
> 11 9 1 12 1 180 4.6 2
> ; ring_180
> 1 3 5 7 1 180 4.6 2
> 3 5 7 9 1 180 4.6 2
> 5 7 9 11 1 180 4.6 2
> 7 9 11 1 1 180 4.6 2
> 9 11 1 3 1 180 4.6 2
> 11 1 3 5 1 180 4.6 2
>
>
> --
> ----------------------------------------------------------------------
> Cen-Feng Fu
> Department of Chemical Physics
> University of Science and Technology of China
> Hefei, Anhui, 230026, P.R.China
> ----------------------------------------------------------------------
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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