Eng's Notebook

Molecular dynamics (MD) simulation is one of the most essential in materials science, as it allows researchers to analyze atomic-scale interactions with high precision. The most widely used MD simulation package is LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). This article provides an in-depth explanation of the structure of a typical LAMMPS input script. It usually has four parts. Initialization System definition Simulation settings Run the simulation 1. Initialization The initialization section sets the basic properties of the simulation. Some of the relevant commands are units, atom_style, and boundary.  units style The style can be real, lj, metal, si, cgs, nano, electron, or micro. Ex: units real This command sets the unit style for the simulation. It determines how input and output values ​​are represented. It affects quantities like mass, distance, energy, and time. atom_style style  Style can be atomic, bond, charge, full, or molecular. Ex: atom_s...

  Hello and welcome to the fourth article in Eng's Notebook! In this article, let's explore the MD (Molecular Dynamics) simulation, focusing on how LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) can be a powerful tool for enhancing your simulations. As an extra point, let's discuss how we can use Linux-based HPC (high-performance computing) for running simulations efficiently, according to my personal experience. 💡 So, what is molecular dynamics? Molecular dynamics (MD) is a computational simulation technique used to study the behavior of atoms and molecules. It allows for the observation of their interactions and movements over a specified period, providing insights into the dynamic evolution of a system.  In most of the industries, the trial-and-error method is used to solve the problem. It can be an extremely time and resource consuming method. When we use a trial and error method, we can't understand what is happening inside the materials and ca...