Molecular dynamics simulation of confined fluids in isosurface-isothermal-isobaric ensemble

Abstract

A method for the simulation of fluids confined between surfaces is developed. The molecular dynamics, with coupling to an external bath, simulation method of Berendsen et al. [J. Chem. Phys. 81, 3684 (1984)] is extended for this purpose. We keep the temperature and the parallel component of pressure fixed and change the box length in the perpendicular direction with respect to the confining surfaces to archive equilibrium. The simulation is easy to perform, especially in the case of solvation force computation. Employing this method, the simulation results on the confined Lennard-Jones and water are presented and are compared to previous grand canonical ensemble Monte Carlo and molecular dynamics simulation results. While consistent with other methods, our results show that spherical Lennard-Jones particles and water form layered structures parallel to the confining surfaces with enhanced layering with increasing pressure. Also we studied the oscillatory behaviors of solvation force and number density of confined particles as well as the stepwise variation of particle numbers as a function of separation between confining surfaces.

Anisotropic heat transport in nanoconfined polyamide-6,6 oligomers: Atomistic reverse nonequilibrium molecular dynamics simulation

“…Such a coupling to a barostat is done through scaling the z-coordinates of all particles per time step, as it is explained in Ref. 31. In this method the distance between the surfaces is changed dynamically to keep P fixed.…”

“…To simulate nanoconfined polyamide-6,6 oligomers (trimers), we have employed our recent simulation scheme, 31 in which a constant number of polymer chains, N, is confined between two parallel surfaces of constant surface area, A, at a constant temperature, T, and a constant parallel component of pressure, P . The details of this method, the so-called NAPT ensemble simulation method, can be found elsewhere; 31 just a brief explanation is given here.…”

“…Equilibrium MD simulations are performed employing the NAPT ensemble simulation method. 31 Choosing a relaxed configuration of the system, RNEMD simulations are done to impose heat flux between polymer layers, perpendicular to the surfaces. A snapshot of the simulation box is shown in Fig.…”

Investigation of the interface between polyethylene and functionalized graphene: A computer simulation study

“…The oscillations in the solvation force curve correspond to the ordering/disordering of the formed layers that are parallel to the surfaces [42,43]. Strong layering behavior at the interface resulted in sharper density peaks corresponds to more repulsive solvation forces [44].…”

Protocol for classical molecular dynamics simulations of nano-junctions in solution

“…Although classical MD studies in the "isosurface-isothermal-isobaric" ensemble (NAPT) 12,13 deal with systems of confined liquids and are computationally efficient, they are not practical to use for answering the above question. Therefore, we attempt to establish a methodology that can be used as a preliminary step for the ab initio modeling.…”