normal Mapping of Benzene Ring

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2 years 3 months ago #8303 by Hot
Mapping of Benzene Ring was created by Hot
In version 2.2, benzene rings are mapped to three SC5 beads, each of which is a three-to-one (C-C=C)mapping.
In version 3.0, the benzene ring is mapped to three TC4 beads, and the bond length is changed from 0.24 to 0.29. Is this a three-to-one mapping or a two-to-one mapping?

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2 years 3 months ago #8304 by riccardo
Replied by riccardo on topic Mapping of Benzene Ring
In version 2.2, benzene is indeed mapped with three SC5 beads, but being benzene made of 6 carbon atoms, I would rather say that that is a 2-to-1 mapping, i.e., two carbon atoms - to - one SC5 bead. Note also that the bond length of benzene is 0.27 nm in Martini 2.2 cgmartini.nl/images/parameters/ITP/martini_v2.0_solvents.itp .

In the open-beta of Martini 3.0, benzene is indeed mapped with three TC4 beads, and that's again a 2-to-1 mapping. The bond length is changed to 0.29 nm in 3.0 because this allows to represent more closely the volume of a benzene molecule, taking into account also the smaller size of T-beads as compared to S-beads.

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2 years 3 months ago #8305 by Hot
Replied by Hot on topic Mapping of Benzene Ring
Thanks for your explanation, I will map the benzene to three 3-to-1 beads in the mapping file.

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