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

J. B. Abrams, Mark 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: From Materials to Chemical Biology Volume 1
Pages139-192
Number of pages54
Volume703
DOIs
StatePublished - 2006

Publication series

NameLecture Notes in Physics
Volume703
ISSN (Print)00758450

Fingerprint

polypeptides
statistical mechanics
free energy
molecular dynamics
paradoxes
chemistry
proteins
simulation

ASJC Scopus subject areas

  • Physics and Astronomy (miscellaneous)

Cite this

Abrams, J. B., Tuckerman, M., & Martyna, G. J. (2006). Equilibrium statistical mechanics, non-hamiltonian molecular dynamics, and novel applications from resonance-free timesteps to adiabatic free energy dynamics. In Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1 (Vol. 703, pp. 139-192). (Lecture Notes in Physics; Vol. 703). https://doi.org/10.1007/3-540-35273-2_5

Equilibrium statistical mechanics, non-hamiltonian molecular dynamics, and novel applications from resonance-free timesteps to adiabatic free energy dynamics. / Abrams, J. B.; Tuckerman, Mark; Martyna, G. J.

Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1. Vol. 703 2006. p. 139-192 (Lecture Notes in Physics; Vol. 703).

Research output: Chapter in Book/Report/Conference proceedingChapter

Abrams, JB, Tuckerman, M & Martyna, GJ 2006, Equilibrium statistical mechanics, non-hamiltonian molecular dynamics, and novel applications from resonance-free timesteps to adiabatic free energy dynamics. in Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1. vol. 703, Lecture Notes in Physics, vol. 703, pp. 139-192. https://doi.org/10.1007/3-540-35273-2_5
Abrams JB, Tuckerman M, Martyna GJ. Equilibrium statistical mechanics, non-hamiltonian molecular dynamics, and novel applications from resonance-free timesteps to adiabatic free energy dynamics. In Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1. Vol. 703. 2006. p. 139-192. (Lecture Notes in Physics). https://doi.org/10.1007/3-540-35273-2_5
Abrams, J. B. ; Tuckerman, Mark ; Martyna, G. J. / Equilibrium statistical mechanics, non-hamiltonian molecular dynamics, and novel applications from resonance-free timesteps to adiabatic free energy dynamics. Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1. Vol. 703 2006. pp. 139-192 (Lecture Notes in Physics).
@inbook{7c9f57ed7d144394becedd3bfdb23fa9,
title = "Equilibrium statistical mechanics, non-hamiltonian molecular dynamics, and novel applications from resonance-free timesteps to adiabatic free energy dynamics",
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.",
author = "Abrams, {J. B.} and Mark Tuckerman and Martyna, {G. J.}",
year = "2006",
doi = "10.1007/3-540-35273-2_5",
language = "English (US)",
isbn = "3540352708",
volume = "703",
series = "Lecture Notes in Physics",
pages = "139--192",
booktitle = "Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1",

}

TY - CHAP

T1 - Equilibrium statistical mechanics, non-hamiltonian molecular dynamics, and novel applications from resonance-free timesteps to adiabatic free energy dynamics

AU - Abrams, J. B.

AU - Tuckerman, Mark

AU - Martyna, G. J.

PY - 2006

Y1 - 2006

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=33947266386&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33947266386&partnerID=8YFLogxK

U2 - 10.1007/3-540-35273-2_5

DO - 10.1007/3-540-35273-2_5

M3 - Chapter

AN - SCOPUS:33947266386

SN - 3540352708

SN - 9783540352709

VL - 703

T3 - Lecture Notes in Physics

SP - 139

EP - 192

BT - Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1

ER -