Uploads by John Chodera
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This special page shows all uploaded files.
| Date | Name | Thumbnail | Size | Description | Versions |
|---|---|---|---|---|---|
| 17:39, 9 October 2007 | Alchemistry.jpg (file) |  |
28 KB | Alchemistry.org logo. | 1 |
| 14:44, 22 December 2013 | Hamiltonian-exchange-reduced-potential.png (file) |  |
51 KB | Reduced potential as a function of iteration for Hamiltonian exchange simulation, computed as : <math> u(X_t) = \sum_{k=1}^K u_{s_{kt}}(x_{kt}) </math> where <math>u_i(x)</math> is the reduced potential for thermodynamic state index <math>i</math> and ... | 1 |
| 16:03, 22 December 2013 | Automated-equilibration-detection.png (file) |  |
38 KB | Top: Statistical inefficiency <math>g</math>. Bottom: Number of effectively uncorrelated samples <math>N_{eff}</math>. | 1 |
| 19:50, 22 December 2013 | Replica-round-trips.png (file) |  |
55 KB | Illustration of three replica trajectories in thermodynamic state index (y-axis) plotted as a function of simulation time (x-axis) for a Hamiltonian exchange absolute alchemical free energy calculation for p-xylene binding to T4 lysozyme L99A. | 1 |
| 20:04, 22 December 2013 | Gelman-rubin.png (file) |  |
18 KB | 1 | |
| 20:05, 22 December 2013 | Gelman-rubin-z-score.png (file) |  |
15 KB | 1 | |
| 20:35, 22 December 2013 | Hindered-sidechain-torsion.png (file) |  |
19 KB | Replica trajectories for the <math>\chi_1</math> angle of T4 lysozyme L99A binding to p-xylene in a Hamiltonian exchange simulation of an absolute alchemical free energy calculation in implicit solvent. | 1 |
| 10:48, 15 May 2016 | Merck Serono postdoctoral researcher for predictive models in drug design.pdf (file) |  |
517 KB | Merck Serono postdoctoral researcher for predictive models in drug design - 2016-06-15 | 1 |
| 10:50, 15 May 2016 | Merck Serono postdoctoral researcher in computational chemistry and molecular dynamics.pdf (file) | |
515 KB | Merck Serono postdoctoral researcher in computational chemistry and molecular dynamics - 2016-05-15 | 1 |
| 12:09, 15 May 2016 | VertexComputationalChemist JobFlyer.pdf (file) | |
242 KB | Vertex - Research Scientist I, Computational Chemist/Modeling and Informatics (posted 2016-05-15) | 1 |
| 14:11, 20 May 2016 | YANK-tutorial-2016-05-20.pdf (file) | |
424 KB | YANK tutorial slides presented at 2016 Markov state models and kinetics in drug discovery workshop at Novartis. | 1 |
