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Updated: Apr 7, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
Published on: September 17, 2021
A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and
Ivan Korotkin1, Sergey Karabasov1, Dmitry Nerukh2
1The School of Engineering and Material Science, Queen Mary University of London, Mile End Road, E1 4NS London, United Kingdom.
Abstract:
A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported.
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