Parameterization of the Coarse-Grained Force Field

The parameterization of CG force fields is not trivial. For the CG study of complex systems such as CLs, the loss of atomistic detail is a real drawback. In fact, this difficulty is not specific to the system under study in this work, but it applies to classical atomistic and coarse-grained molecular modeling. Employing these methods relies on averaging out microscopic degrees of freedom. Electronic structure effects are not explicitly treated. These limitations are well apprehended (Markvoort, 2010). An adequate approach should incorporate essential physicochemical properties of interest, while ignoring certain less important details to keep the calculation computationally viable. 

In the MS-CG scheme described above (Izvekov and Violi, 2006 Izvekov and Voth, 2005 Izvekov et al., 2005), the positions of CG beads and forces Fpp 

Phenomenological CG interaction parameters between Water (W), Hydro-nium ion (H), Backbone (B), Sidechain (S), and Carbon (C) in Carbon Particles 

Note This includes Pt beads, initially used in CGMD simulations, with = Asg and Ci2 = 

The initial simulation box evaluated in Malek et al. (2011) had a size of 500 x 500 x 500 nm. It contained eight PPCs, including in total 416 CNPs and varying numbers 

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