AMBER Archive (2008)

Subject: Re: AMBER: comparison of MD trajectories recorded with pmemd and sander

From: Thomas Cheatham III (
Date: Wed Dec 17 2008 - 11:16:47 CST

> Molecular dynamics trajectories are inherently chaotic. This means that the
> trajectory is extremelly dependent on initial conditions.

...I always like to point people to the Braxenthaler/Moult article:

  Braxenthaler et al. "Chaos in protein dynamics" Proteins 29, 417-425 (1997)

Also, perhaps:

  Nerukh et al. "Complexity of classical dynamics of molecular systems.
  II. Finite statistical complexity of a water-Na+ system." J Chem Phys
  117, 9618 (2002)

  Cooke/Schmidler "Statistical prediction and molecular dynamics
  simulation" Biophys J 95, 4497-4511 (2008).

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