Construction of Multi-Scale Dissipative Particle Dynamics (DPD) Models from other Coarse-Grained Models

We present a general scheme for converting coarse grained models into Dissipative Particle Dynamics (DPD) models. We build the corresponding DPD models by anal- ogy with the de novo DPD coarse graining scheme suggested by Groot and Warren (J. Chem. Phys., 1997). Electrostatic interactions between charged DPD particles are represented though the addition of a long-range Slater Coulomb potential as suggested by Gonz ́alez-Melchor et al (J. Chem. Phys 2006). The construction is illustrated by converting MARTINI models for various proteins into a DPD representation, but it not restricted to the usual potential form in the MARTINI model—viz Lennard-Jones potentials. We further extended the DPD scheme away from the typical use of homo- geneous particle sizes, and therefor faithfully representing the variations in the particle sizes seen in the underlying MARTINI model. The accuracy of the resulting construc- tion of our generalized DPD models with respect to several structural observables have been benchmarked favorably against all-atom and MARTINI models for a selected set of peptides and proteins, and variations in the scales of the coarse-graining of the water solvent.