History of molecular dynamics simulation

Brief History of Computer Simulations

•1953:Equation of state calculations by fast computing mechines (1953)

Nicholas_Metropolis_croppedN Metropolis,A W Rosenbluth, M N Rosebluth, A H Teller

This paper applied Monte-Carlo technique to solving physical equations of a system composed of interacting individual molecules. First step is to generate a subset of random number to represent conformational space, then using exponent of the energy as probability filter.

• 1956: Phase Transition for a Hard Sphere System

Berni_AlderB. J. Alder and T. E. Wainwright
– First “proper” molecular dynamics (MD) simulation: dynamics of an
assembly of hard spheres

• (1958: A three-dimensional model of the myoglobin molecule obtained by x-ray analysis)

myoglobinFirst X-ray structure of protein

• 1964: Correlations in the Motion of Atoms in Liquid Argon

A. RahmanA. Rahman  
– MD simulation of liquid Ar.  He is known as the father of molecular dynamics

• 1969: Barker and Watts
– Monte Carlo simulation of water
• 1971: Rahman and Stillinger
– MD simulation of water
• Water simulations are a greater challenge than liquid Ar since,
in addition to van der Waal’s interactions, there are Coulomb
and hydrogen bond interactions.

1970s: Simulations of small solutes and peptides

•1975 Computer simulation of protein folding

Michael Levitt Arich Warshel

First published MD simulation of protein, and sucessfully refold BPTI from an open-chain conformation(terminal helix) by simplifiled representation of protein structure.

• 1977: McCammon, Gelin, Karplus
First MD simulation of proteins
– Simulations of biomolecules
– Free energy calculations
– Protein-ligand docking calculations

• 1979:Dynamics of ligand binding to heme protein

D A Case, M Karplus

-This is the first simulation of ligand moving through the protein.

• 1988:Accurate simulation of protein dynamics in solution

Michael Levitt and R Sharon

- First simulation of a protein in explicit waters.
• 1990s:
– Continued development of potentials and sampling techniques
• 1998: Duan and Kollman: 1µs MD simulation of the folding of
the Villin headpiece in explicit solvent
• 1999: Sugita and Okamoto: replica exchange molecular