Easy and Fast Setup of Molecular Dynamics Simulations: Combining VMD and NAMD for Experimentalists

Abstract

The relationship between structure and function of proteins is directly connected to atomistic aspects of protein dynamics. As a major methodology in structural biology, molecular dynamics (MD) simulations permit the exploration of the physical mechanism underlying the function of proteins by examining their dynamical behavior. Although the advances in MD simulations are leading to a new level of knowledge of macromolecular complexes, reaching the million-to-billion atom regime (1), the vast majority of MD users are interested in straightforward MD simulations of relatively simple proteins. Particularly in the last few years, structural biology experimentalists’ interest in performing MD simulations to improve their knowledge of a protein structure/function relationship has increased greatly. To assist these experimentalists and any novice to MD to overcome the initial learning curve barrier of MD simulation software, we developed a user interface (plugin) that connects the widely employed and user-friendly molecular graphics program VMD to the widely adopted MD program NAMD. Employing this plugin, a user is able to setup an MD simulation in just a few minutes, allowing quick studies of point mutations, partial deletions and even atomic force microscopy experiments. The plugin makes it easy for a new user to perform MD simulations, while it also servers as a learning tool. Many “info buttons” provide the theoretical background underlying the MD procedures carried out in modern MD simulations.1. Perilla, J.R., et al. 2015. Molecular dynamics simulations of large macromolecular complexes. Curr. Opin. Struct. Biol. 31: 64-74.