I find myself constantly working with computers on a daily basis…and NO I am not a developer or technician. My computer skills are about on par with your average Joe who typically knows how to turn a computer off and on. Maybe I know a bit more than that. Nevertheless, in my lab I am surrounded by colleagues who can code in multiple languages, design apps, websites, and software etc. This has inspired me to learn computer programming and as a result I have developed some level of interest in coding and scripting.
Given that I am constantly performing molecular simulations on biomolecules like proteins and amino acids, I find that scripting repetitive tasks like energy minimization and system equilibrations often saves time for other important tasks like keeping up to date with current research/literature, which are very essential as a researcher. Okay, so the main goal of this post is to summarize my recent readings about molecular dynamics; which is a method I constantly use in my research for gaining insights into the structure and dynamics of proteins.
Molecular Dynamics (MD) – the science of simulating the motions of a system of particles – serves a pivotal role in molecular biology [1] providing critical insights into the structure, function and thermodynamics of biological molecules. This computational methodology gives route to the dynamical properties (i.e. time-dependent behaviour) of a molecular system by solving Newton’s equation of motion, from which trajectories for all atoms in the system are collected. Knowledge of these atomic motions provides valuable information regarding molecular processes and is fundamental to the calculation of a wide array of inherent physicochemical properties of a molecular system.
The MD simulation technique was primarily introduced by Berni J. Alder and Thomas E. Wainwright in the mid-1950’s to study the interaction of classical particles and the phase transition of hard spheres.[2, 3] Other significant advancements have since followed from the pioneering works of Rahman,[4] Stillinger,[5] Verlet,[6] and Karplus.[7] These groundbreaking contributions together with the dramatic progress in computer technology and algorithmic developments, have paved the way for the present-day revolution of MD simulations.
References for further reading
- Karplus, M.; Petsko A. G. Molecular Dynamics Simulations in Biology. Nature, 1990, 347, 631–639.
- Alder, B. J.; Wainwright,T. E. Studies in Molecular Dynamics. I. General Method. J. Chem. Phys. 1959, 31, 459–466.
- Alder, B. J.; Wainwright, T. E. Phase Transition for a Hard Sphere System. J. Chem. Phys. 1957, 27, 1208–1209.
- Rahman, A. Correlation in the Motion of Atoms in Liquid Argon Phys. Rev., 1964, 136, 405–411.
- Stillinger, F. H.; Rahman, A. Molecular Dynamics Study of Liquid Water under High Compression J. Chem. Phys., 1975, 61, 4973–4980.
- Verlet, L. Computer “Experiments” on Classical Fluids I. Thermodynamic Properties of Lennard-Jones Molecules* Phys. Rev., 1967, 159, 98–103.
- McCammon, A. J.; Gelin, R. B.; Karplus, M. Dynamics of Folded Proteins. Nature, 1977, 267, 585–590.