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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
Protein Contact Maps
22 Oct 2010 | Tools | Contributor(s): Benjamin Rafferty, Zachary Carl Flohr, Ashlie Martini
Create and view protein contact maps and distance maps.
Addressing Molecular Dynamics Time-scale Issues to Study Atomic-scale Friction
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...
Lecture 10: Non Equilibrium MD
05 Jan 2010 | Presentation Materials | Contributor(s): Ashlie Martini
Topics:Calculating transport coefficientShear flowPerturbation methods
Lecture 9: Dynamic Properties
Topics:Time correlation functionsEinstein relationsGreen-Kubo relations
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