TITLE

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules

AUTHOR(S)
Hamelberg, Donald; Mongan, John; Mccammon, J. Andrew
PUB. DATE
June 2004
SOURCE
Journal of Chemical Physics;6/22/2004, Vol. 120 Issue 24, p11919
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution. ©2004 American Institute of Physics.
ACCESSION #
13361775

 

Related Articles

  • Molecular Dynamics Simulation Using Gupta Potential Energy Function of “Superheated” Small Nickel Clusters. Bayhan, Ü.; Çivi, M. // AIP Conference Proceedings;2007, Vol. 899 Issue 1, p558 

    Fragmentation behaviour of nonrotating “superheated” small Nin, n=4–5 clusters have been studied with molecular dynamics simulations using Gupta potential energy function. Survival probabilities and global fragmentation rate constants are computed and analysed as functions of...

  • General relationships between the mobility of a chain fluid and various computed scalar metrics. Budzien, Joanne; McCoy, John D.; Adolf, Douglas B. // Journal of Chemical Physics;11/22/2004, Vol. 121 Issue 20, p10291 

    We performed molecular dynamics simulations of chain systems to investigate general relationships between the system mobility and computed scalar quantities. Three quantities were found that had a simple one-to-one relationship with mobility: packing fraction, potential energy density, and the...

  • Multicanonical ensemble with Nose´–Hoover molecular dynamics simulation. Jang, Soonmin; Pak, Youngshang; Shin, Seokmin // Journal of Chemical Physics;3/22/2002, Vol. 116 Issue 12, p4782 

    We demonstrate that molecular dynamics simulations using the force scaling method with a Nosé— Hoover-chain thermostat are capable of generating multicanonical ensembles. The frequency distribution of the Nosé—Hoover-chain is broad enough to handle the energy dependent force...

  • Formation ofmolecules with sub-kelvin translational energy via molecular beam collisions with argon using the technique of molecular cooling by inelastic collisional energy-transfer. Elioff, M.; Valentini, J.; Chandler, D. // European Physical Journal D -- Atoms, Molecules, Clusters & Opti;Nov2004, Vol. 31 Issue 2, p385 

    We report the cooling of nitric oxide molecules in a single collision between an argon atom and an NO molecule at collision energies ofkJ/mol andkJ/mol in a crossed molecular beam apparatus. We have produced in significant numbers (~108 molecules cm-3 per quantum state) translationally cold...

  • Calculation of solid-liquid interfacial free energy: A classical nucleation theory based approach. Xian-Ming Bai; Mo Li // Journal of Chemical Physics;3/28/2006, Vol. 124 Issue 12, p124707 

    We present a simple approach to calculate the solid-liquid interfacial free energy. This new method is based on the classical nucleation theory. Using the molecular dynamics simulation, we employ spherical crystal nuclei embedded in the supercooled liquids to create an ideal model of a...

  • Ab initio molecular dynamics simulation of the Cu(110)-water interface. Izvekov, Sergei; Mazzolo, Alain; VanOpdorp, Kirk; Voth, Gregory A. // Journal of Chemical Physics;2/15/2001, Vol. 114 Issue 7 

    The results of a first principles simulation of the Cu(110)-water interface are presented. The calculations were carried out using ab initio Car-Parrinello molecular dynamics simulation within a pseudopotential formalism and the BLYP generalized gradient approximation to the exchange-correlation...

  • Segmental dynamics and relaxation of n-octane at solid–liquid interfaces. Gupta, S.; Koopman, D. C.; Westermann-Clark, G. B.; Bitsanis, I. A. // Journal of Chemical Physics;6/1/1994, Vol. 100 Issue 11, p8444 

    In this paper we present our results from a molecular dynamics study of n-octane liquids confined between planar bcc solid surfaces. The systems studied were wide enough to develop a bulklike region throughout the middle portion of the film and two well-separated interfaces. Our work focused on...

  • Nonequilibrium molecular dynamics simulations of confined fluids in contact with the bulk. Zhang, Luzheng; Balasundaram, Ramkumar; Gehrke, Stevin H.; Jiang, Shaoyi // Journal of Chemical Physics;4/15/2001, Vol. 114 Issue 15 

    A nonequilibrium molecular dynamics (MD) simulation study is reported of the structural and rheological properties of confined n-decane between two Au(111) surfaces in contact with its bulk under constant normal loads or constant heights. In the constant-load MD simulations, it was observed that...

  • Molecular dynamics of phenol at the liquid–vapor interface of water. Pohorille, Andrew; Benjamin, Ilan // Journal of Chemical Physics;4/15/1991, Vol. 94 Issue 8, p5599 

    Molecular dynamics results are presented for phenol at the water liquid–vapor interface at 300 K. The calculated excess free energy of phenol at the interface is -2.8±0.4 kcal/mol, in good agreement with the recent experimental results of Eisenthal and co-workers. The most probable...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics