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 the assumptions that the system being modeled advances to new configurations via infrequent events and that there are well-defined instantaneous rate constants for these events that are independent of the driving rate.
09 Nov 2009 | Tools | Contributor(s): Ashlie Martini, Jianguo Wu
Molecular dynamics simulation of atomic stick-slip friction
Lecture 10: Non Equilibrium MD
05 Jan 2010 | Presentation Materials | Contributor(s): Ashlie Martini
- Calculating transport coefficient
- Shear flow
- Perturbation methods