Making Classical and Hybrid (QM/MM) Molecular Dynamics Easy and Fast with QwikMD

Abstract

“Everything that living things do can be understood in terms of jigglings and wigglings of atoms.” Richard Feynman's remarks in the early 1960's summarize what is today widely accepted, namely, that molecular processes can be described by the dynamics of biological molecules, therefore connecting protein function with protein dynamics. Molecular dynamics (MD) simulation, in this regard, is the major methodology employed in structural biology to explore the dynamical behavior of macromolecules. Although the use of MD simulations has consistently increased over the last decades, the barrier imposed by the initial learning curve of the MD packages is still high. To assist new users in overcoming this barrier, and to help the more advanced users to speed up tedious preparation steps, we developed QwikMD(1). This user-friendly program connects the widely used molecular graphics program VMD to the widely adopted MD program NAMD. Employing QwikMD, a user is able to setup an MD simulation in just a few minutes, allowing quick studies of point mutations, partial deletions or even atomic force microscopy experiments. Within the different modules of QwikMD, one can adopt a myriad of simulation protocols, from single protein in vacuum to hybrid QM/MM simulations. QwikMD makes it easy for a new user to perform MD simulations, while it also serves as a learning tool. Many “info buttons” provide the theoretical background underlying the MD procedures carried out in modern MD simulations.1. J. V Ribeiro et al., QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts. Sci. Rep. 6, 26536 (2016).