Welcome to Molecular Simulation Basics!#
Welcome to this tutorial focused on the fundamentals of molecular simulation. We will discuss background theories, force-fields, simulation setup, specific techniques, how to write post-processing codes, statistics and errors, common pitfalls, etc. In this particular workflow, we specifically take the commonly used MD package LAMMPS. Our aim is to provide you with a comprehensive understanding of computational techniques essential for molecular dynamics research.
Objectives:
Introduction to LAMMPS: This tutorial will commence with an introductory overview of LAMMPS, a prominent molecular dynamics simulation software. You will familiarize yourself with its interface and learn the essential commands and syntaxes required for conducting simulations.
Practical Application: Through hands-on exercises, we will engage in the practical implementation of simulation setups, parameter definition, and result analysis. This interactive approach ensures a thorough comprehension of the simulation process. In addition to simulation execution, emphasis will be placed on mastering post-processing techniques. Throughout the chapters, we will be equipped with the skills to develop custom post-processing codes, facilitating in-depth analysis and interpretation of simulation data.
Exploration Opportunities: We explore topics ranging from simple fluid systems and single polymer chains to advanced simulation methodologies. We explore codes from online repositories, which have been previously benchmarked, to evaluate our capability to reproduce results.
Visualization: For visualization tools, we primarily utilize OVITO, which offers excellent visualization capabilities. These capabilities include generating high-quality movies and simulation snapshots suitable for use in academic papers. OVITO Pro also provides convenient post-processing properties such as surface generation, histograms, correlation analysis, radial distribution functions, and particle selection.
Contact Details#
Email: subhadip@iastate.edu
LinkedIn: linkedin.com/in/biswas-subhadip
Twitter: @subhadip_shuvo