Extending Hamiltonian-Adaptive Resolution Simulation to Interfaces: An Updated LAMMPS Implementation and Application to Porous Solids

Abstract

Many natural phenomena involve processes that happen simultaneously at different characteristic length- and timescales. Typically, the region where the process of interest happens is affected by fluctuations in its surroundings. Modeling these systems requires an effective combination of simulation resolutions. The Hamiltonian-Adaptive Resolution Simulation (H-AdResS) method allows to model dual-resolution systems in length- and time-scales compatible with molecular diffusion, by combining atomistic and particle-based coarse graining models in the same simulation box. In this work, a new implementation of H-AdResS is provided in LAMMPS 2023. New features extend the usage to more diverse interaction potentials and simplify the preparation of input files via dedicated lammps input commands, while keeping the efficiency gain of the basis method. The implementation is benchmarked by reproducing water properties from a reference atomistic simulation. Importantly, the new implementation includes changes in compensation routines allowing to simulate systems with fluctuating density. As an example, the method in its new implementation is applied to modeling a porous metal-organic framework and its gas adsorption structure and transport properties. We demonstrate that structural and dynamic properties in the atomistic region of the dual-resolution scheme are unaffected and remain those of the fully atomistic system, while increasing simulation efficiency. This paves the way for using H-AdResS to simulate complex interfaces across applications in energy storage, electrocatalysis, and membrane technologies.

16 pages, 12 figures

References in corpus (12)

• Adaptive Resolution Molecular Dynamics Simulation: Changing the Degrees of Freedom on the Fly
• Hamiltonian adaptive resolution simulation for molecular liquids
• Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir
• Automatic Coarse Graining of Polymers
• A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site
• Adaptive Resolution Molecular Dynamics Technique: Down to the Essential
• Probing Spatial Locality in Ionic Liquids with the Grand Canonical Adaptive Resolution Molecular Dynamics Technique
• Coarse Grained modeling of Zeolitic Imidazolate Framework-8 using MARTINI Force Fields
• Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique
• Force Matching and Iterative Boltzmann Inversion Coarse Grained Force Fields for ZIF-8
• Coarse grained modeling of a metal-organic framework/polymer composite and its gas adsorption at the nanoparticle level
• MARTINI-based force fields for predicting gas separation performances of MOF/polymer composites