gmx-users, Dear all, I make a *.itp for benzene by myself. All parameters come from the ffoplsaabon.itp and ffoplsaanb.itp. while I have some puzzled about the dihedral parameters of benzene. In ffoplsaabon.itp file, there are dihedral parameters of benzene and the potential function is 3, like this: ;X CA CA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring
but for improper dihedral of benzene there is some another dihedral parameters of benzene and the potential function is 1,like this: ; Z -CA-X -Y improper torsion. CA is any ring carbon #define improper_Z_CA_X_Y 1 180.0 4.60240 2 I think the improper dihedral can keep the molecule of benzene planar. So I have no idea how to set dihedral the parameters of benzene. I tryto make a BEN.itp like this, but I don't know if it is correct. [ moleculetype ] ; Name nrexcl BEN 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 CA 1 BEN C1 1 -0.205 2 CA 1 BEN C2 2 -0.205 3 CA 1 BEN C3 3 -0.205 4 CA 1 BEN C4 4 -0.205 5 CA 1 BEN C5 5 -0.205 6 CA 1 BEN C6 6 -0.205 7 HA 1 BEN H7 1 0.205 8 HA 1 BEN H8 2 0.205 9 HA 1 BEN H9 3 0.205 10 HA 1 BEN H10 4 0.205 11 HA 1 BEN H11 5 0.205 12 HA 1 BEN H12 6 0.205 [ bonds ] ; i j func length force.c 1 2 1 0.13942 392459.2 1 6 1 0.13942 392459.2 ... ... [ angles ] ; i j k func angle force.c 2 1 6 1 120.000 527.184 2 1 7 1 120.000 292.880 ... ... [ dihedrals ] ; i j k l func c0 c1 c2 c3 c4 c5 6 1 2 3 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 6 1 2 8 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 7 1 2 3 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 7 1 2 8 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 2 1 6 5 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 2 1 6 12 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ... ... [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 7 1 2 6 1 180.0 4.60240 2 8 2 3 1 1 180.0 4.60240 2 9 3 2 4 1 180.0 4.60240 2 10 4 3 5 1 180.0 4.60240 2 11 5 4 6 1 180.0 4.60240 2 12 6 5 1 1 180.0 4.60240 2 Jinyao Wang wan...@ciac.jl.cn 2009-05-25
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