Simulation methods

This page collects the molecular dynamics (MD) simulation details for the systems presented throughout this documentation. Each application or validation page links back here rather than repeating the full setup, so that simulation parameters are documented in a single, consistent location.

Lennard-Jones fluid

The simulated system contains 16,000 particles interacting through the classical Lennard–Jones (12-6) potential and was simulated using LAMMPS [45]. Each particle has a mass \(m = 1\,\mathrm{g/mol}\) together with LJ parameters \(\sigma = 3\,\text{Å}\) and \(\epsilon = 0.1\,\mathrm{kcal/mol}\). All reduced simulation parameters were chosen to reproduce the study of Grivet [6]. In particular, the interaction cutoff was set to \(4 \sigma\), while the cubic simulation box had a side length of \(26.9 \sigma\), corresponding to the reduced density \(\rho^*=0.84\). Production runs were performed in the microcanonical (NVE) ensemble, during which 10,000 timesteps were executed, equivalent to 50 times the reference time \(\sqrt{m \sigma^2/\epsilon}\). Configurations were recorded every 10 timesteps. A timestep of \(0.005\,\sqrt{m \sigma^2/\epsilon}\) was used. The imposed temperatures ranged from \(T = 30\) to \(160\,\text{K}\), corresponding to reduced temperatures from \(T^* = 0.8\) to \(3.0\).

Reduced Lennard–Jones units

Lennard-Jones simulations are commonly expressed in reduced units, where the particle mass \(m\), the characteristic length \(\sigma\), and the interaction energy \(\epsilon\) define the natural scales of the system. Using reduced variables allows simulations with different physical parameters to be compared directly.