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? 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. > sp...@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 ----------------------------------------------------------------------
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