Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs

Sumit Sharma

• Publisher: Elsevier
• Year: 2019
• Print ISBN: 9780128169544
• eBook ISBN: 9780128169551
• Topic: Technology & Engineering
• Subtopic: Materials Science
• Index: Technology & Engineering

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs presents the three major software packages used for the molecular dynamics simulation of nanocomposites. The book explains, in detail, how to use each of these packages, also providing real-world examples that show when each should be used. The latter two of these are open-source codes which can be used for modeling at no cost. Several case studies how each software package is used to predict various properties of nanocomposites, including metal-matrix, polymer-matrix and ceramic-matrix based nanocomposites. Properties explored include mechanical, thermal, optical and electrical properties. This is the first book that explores methodologies for using Materials Studio, Lammps and Gromacs in the same place. It will be beneficial for students, researchers and scientists working in the field of molecular dynamics simulation. - Gives a detailed explanation of basic commands and modules of Materials Studio, Lammps and Gromacs - Shows how Materials Studio, Lammps and Gromacs predict mechanical, thermal, electrical and optical properties of nanocomposites - Uses case studies to show which software should be used to solve a variety of nanoscale modeling problems

Chapter 1

Introduction to Molecular Dynamics

Sumit Sharma; Pramod Kumar; Rakesh Chandra Department of Mechanical Engineering, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, India

Abstract

This chapter provides the reader an initial overview of molecular dynamics (MD). Various molecular modeling methods such as MD, Monte Carlo, Brownian dynamics, dissipative particle dynamics, and lattice Boltzmann methods have been discussed to highlight how these are different from each other. Types of force field, potential, ensemble, thermostat, boundary conditions, and MD methodology have been discussed in detail for better understanding of the readers. The readers are suggested to go through the references given at the end of this chapter for advanced reading. After reading this chapter the audience will be able to understand the basic terminology of molecular modeling.

Keywords

Molecular dynamics; Force field; Potentials; Thermostats; Boundary conditions

In the modern nanotechnology age, microscopic analysis methods are necessary to generate new functional materials and investigate physical phenomena on a molecular level. In these methods the constituent species of a system, such as molecules and fine particles, are considered. Macroscopic and microscopic quantities of interest are derived from analyzing the behavior of these species. These approaches, called “molecular simulation methods,” are represented by the Monte Carlo (MC) and molecular dynamics (MD) methods. MC methods exhibit a powerful ability to analyze thermodynamic equilibrium but are unsuitable for investigating dynamic phenomena. MD methods are useful for thermodynamic equilibrium but are more advantageous for investigating the dynamic properties of a system in a nonequilibrium situation. Besides the earlier stated methods, there exist other methods also that can be used to investigate the physical phenomenon on a molecular level. Some of these are as follows:

1. (i) BD methods, which can simulate the Brownian motion of dispersed particles
2. (ii) DPD and lattice Boltzmann methods in which a liquid system is regarded as composed of virtual fluid particles

Simulation methods using the concept of virtual fluid particles are generally used for pure liquid systems but are useful for simulating particle dispersions.

1.1 Molecular Dynamics

The concept of the MD method is straightforward and logical. The motion of molecules is generally governed by Newton's equations of motion in classical theory. In MD simulations, particle motion is simulated on a computer according to the equations of motion. If one molecule moves solely on a classical mechanics level, a computer is unnecessary because mathematical calculation with pencil and paper is sufficient to solve the motion of the molecule. However, since molecules in a real system are numerous and interact...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• Dedication
• Contributors
• Preface
• Chapter 1: Introduction to Molecular Dynamics
• Chapter 2: Overview of BIOVIA Materials Studio, LAMMPS, and GROMACS
• Chapter 3: Molecular Dynamics Simulation of Metal Matrix Composites Using BIOVIA Materials Studio, LAMMPS, and GROMACS
• Chapter 4: Molecular Dynamics Simulation of Polymer-Matrix Composites Using BIOVIA Materials Studio, LAMMPS, and GROMACS
• Chapter 5: Molecular Dynamics Simulation of Ceramic Matrix Composites Using BIOVIA Materials Studio, LAMMPS, and GROMACS
• Chapter 6: Scripting in Molecular Dynamics
• Chapter 7: Applications of BIOVIA Materials Studio, LAMMPS, and GROMACS in Various Fields of Science and Engineering
• Index