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

From: Thomas Cheatham III <>
Date: Wed, 17 Dec 2008 10:16:47 -0700 (Mountain Standard Time)

> 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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Received on Fri Dec 19 2008 - 01:10:00 PST
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