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dihedral parameter
- msaeedi
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10 years 7 months ago #1921
by msaeedi
dihedral parameter was created by msaeedi
Hi,
I want to prepare improper dihedral parameter for a molecule with 3 aromatic rings. I had an AA simulation and measured the dihedral angle for groups of atoms that corresponded to 4 cg beads. The dihedral distribution is u shape and the maximum of the curve in 180 and -180 degree. This distribution is not symmetric, is it wrong? Should I choose 180 or – 180 for this improper dihedral in cg topology?
I want to prepare improper dihedral parameter for a molecule with 3 aromatic rings. I had an AA simulation and measured the dihedral angle for groups of atoms that corresponded to 4 cg beads. The dihedral distribution is u shape and the maximum of the curve in 180 and -180 degree. This distribution is not symmetric, is it wrong? Should I choose 180 or – 180 for this improper dihedral in cg topology?
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- djurre
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10 years 7 months ago #1937
by djurre
Replied by djurre on topic dihedral parameter
improper dihedrals are control the angle between two triangles (ijk vs jkl). An angle of 180 degrees means the same as -180 degrees: the triangles lay in the same plane, with i and l pointing away from their common base. The fact that the distribution is not symmetric might have different reasons. If it is due to non-bonded interactions interfering, it might also show up in you final CG model. If it is something else, it might not be possible to exactly mimic the distribution.
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