Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics

Abstract

Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, bridging the micro- and mesoscopic descriptions. The interfacing is performed within the adaptive resolution scheme (AdResS), which is a linear momentum conserving coupling technique. Our methodology is hence suitable to simulate fluids on the micro/mesoscopic scale, where hydrodynamics plays an important role. The presented approach is showcased for water at ambient conditions. The supramolecular coupling is enabled by a recently developed clustering algorithm SWINGER that assembles, disassembles, and reassembles clusters as needed during the course of the simulation. This allows for a seamless coupling between standard atomistic MD and DPD models. The developed framework can be readily applied to various applications in the fields of materials and life sciences, e.g., simulations of phospholipids and polymer melts, or to study the red blood cells behavior in normal and disease states.

SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids

“…We demonstrate the successful coupling of SPC and MARTINI water models using a 4-to-1 mapping, where we first consider the pure solvent system [70] and later we immerse a protein into this multiscale solvation [71]. Apart from MARTINI, the SPC water model is also coupled to the DPD water model using 4-and 8-to-1 mappings, which unveils the basics of merging the MD and DPD particle-based methods [72].…”

“…Note that in the multiscale setup, there is no need for a continuous SCG trajectory as opposed to the bottom-up SCG [38]. The algorithm was applied to link the AT and the MARTINI SCG force field [70,71], paving the way for efficient biomolecular MD simulations, and also to a concurrent coupling of MD and DPD, thus bridging atomistic and mesoscopic hydrodynamics [72].…”

Multi-resolution dimer models in heat baths with short-range and long-range interactions

“…Equations for coupled detailed/coarse-grained models can be systematically derived using Zwanzig's projection method, which has been used to address co-existence of atoms and beads (larger coarse-grained units) in the same dynamic simulations [72,73]. The equations of motion take the form of dissipative particle dynamics, which have been coupled with atomistic water simulations to design multi-resolution schemes in the literature [74]. Other multi-resolution methods couple atomistic water with specially designed coarse-grained water models [75] or with a continuum approach [35].…”

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

“…Extending the OBMD framework with the TD force, which is needed in our case, means that we are applying an external force to the system, which changes the linear momentum (18). Thus, the linear momentum is not conserved on the local atomistic level, but it is conserved on the fluctuating hydrodynamics level of description, as was shown in (82). Note that our system is radially symmetric; therefore, the applied TD force is also symmetric over the center of the explicit region.…”

“…Note that our system is radially symmetric; therefore, the applied TD force is also symmetric over the center of the explicit region. Hence, for the homogeneous systems (e.g., salt solution), the total momentum would be, because of the symmetry (82), preserved on average even if the last term in Eq. 3 were omitted, i.e.,F ext ¼ J,n B A þ ðP out À P in Þ=Dt.…”