We present a general scheme for converting coarse-grained models into Dissipative Particle Dynamics (DPD) models. We build the corresponding DPD models by analogy 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 González-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 homogeneous particle sizes, therefore faithfully representing the variations in the particle sizes seen in the underlying MARTINI model. The accuracy of the resulting construction of our generalized DPD models with respect to several structural observables has 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.
© 2024 The Authors. Published by American Chemical Society.