1. Frenkel-Kontarova Model

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   11 Jul 2011 | Tools | Contributor(s): Calvin J Mwesigwa, Ashlie Martini

   Simulate movement of simple molecules over a 2D potential energy landscape due to external forcing using the Frenkel-Kontarova model

2. Protein Contact Maps

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   22 Oct 2010 | Tools | Contributor(s): Benjamin Rafferty, Zachary Carl Flohr, Ashlie Martini

   Create and view protein contact maps and distance maps.

3. Addressing Molecular Dynamics Time-scale Issues to Study Atomic-scale Friction

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   total: updated 03 May 2013
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   12 Oct 2010 | Online Presentations | Contributor(s): Ashlie Martini

   This presentation will include an introduction to several accelerated molecular dynamics methods. However, particular focus will be given to parallel replica (ParRep) dynamics in which atomistic simulations are run parallel in time to extend their total duration. The ParRep method is based on the …

4. Atomic Stick-Slip

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   09 Nov 2009 | Tools | Contributor(s): Ashlie Martini, Jianguo Wu

   Molecular dynamics simulation of atomic stick-slip friction

5. Lecture 10: Non Equilibrium MD

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   05 Jan 2010 | Notes | Contributor(s): Ashlie Martini

   Topics: Calculating transport coefficient Shear flow Perturbation methods

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