Equilibrium statistical mechanics, non-hamiltonian molecular dynamics, and novel applications from resonance-free timesteps to adiabatic free energy dynamics

J. B. Abrams, Mark E. Tuckerman, G. J. Martyna

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Levinthal's paradox [1,2], first introduced in the 1960's (early in the childhood of simulations in Chemistry), serves as a good illustration of the limitations we still face in the application of molecular dynamics (MD). Levinthal reasoned that if we were to assume that every residue in a polypeptide has a least two stable conformations, then a small 100 residue polypeptide would have 2 100 possible states. If we were to study such a protein using traditional, state of the art, MD techniques, the native state would only be deduced after a little more than a billion years.

Original languageEnglish (US)
Title of host publicationComputer Simulations in Condensed Matter Systems
Subtitle of host publicationFrom Materials to Chemical Biology Volume 1
EditorsMauro Ferrario, Giovanni Ciccotti, Kurt Binder
Pages139-192
Number of pages54
DOIs
StatePublished - 2006

Publication series

NameLecture Notes in Physics
Volume703
ISSN (Print)0075-8450

ASJC Scopus subject areas

  • Physics and Astronomy (miscellaneous)

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