Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir

Abstract

The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, a combined, explicit reservoir is constructed by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed.Molecular dynamics (MD) simulations have proven as a powerful means of investigation of molecular systems for half a century now. [1] The steady increase of computing resources has brought larger system sizes and longer time scales into the scope of direct simulations, which may soon be run in parallel to experiments. Diverse application fields know about situations where the region of interest exchanges particles with an environment, for example, droplet evaporation, [2] condensation in porous hosts, [3,4] nanoflows, [5] and chemical reactions in

Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation

“…The minimal size of the atomistic region in AdResS which delivers structural properties faithfully reproducing those calculated in a full atomistic simulation of reference defines the region where the atomistic or chemical degrees of freedom are strictly required for the properties analyzed. The technical innovation of this work is the use of the most recent version of AdResS where the majority of the system's reservoir, TR, is represented by noninteracting, pointlike tracer particles with a direct coupling to the transition region [7]. Given the molecular complexity of the system considered in this .…”

“…A water molecule leaving the region and entering the TR region is mapped onto a virtual site whose trajectory corresponds to the dynamics of the tracer while the atoms of the water molecule are rigidly bound to the site and their equations of motion are no longer considered. In our previous work [7] we have shown that for a liquid of pure water at room conditions, the cooperative action of the thermodynamic force and of the thermostat assures proper equilibrium throughout the system and allows for accurate structural and dynamical properties to be calculated in the AT region. The extreme simplification of the computational setup became possible through the mapping of the algorithm onto a theoretical model of open system.…”

“…Simulations were performed with the newest AdResS methodology detailed in Ref. [7] with a modified GROMACS 5.1. The simulation box is divided along the x axis in one AT region, two (transition) regions, and two TR regions which are connected through periodic boundary conditions.…”

“…The thermodynamic force was calculated for a system of pure bulk water, in a procedure similar to that of our previous paper [7]. The same simulation box from the atomistic reference simulation was used and split up into an AT region of x = 10 nm flanked by regions of x = 1.2 nm each with the rest of the box in the x direction represented by tracer particles.…”

The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation

“…Gas molecules are added to and removed from the reservoir in events that resemble GCMC insertion and deletion moves, which fixes the chemical potential (and, hence, the pressure) of the remainder of the simulation cell once the system has adequately equilibrated. Readers can consult work by the group of Parrinello [75–77] for details of the general approach or others [78–80] for specific applications to adsorption of gases in porous materials.…”