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| Date | Name | Thumbnail | Size | User | Description | Versions |
|---|---|---|---|---|---|---|
| 18:39, 9 October 2007 | Alchemistry.jpg (file) |  |
28 KB | John Chodera | Alchemistry.org logo. | 1 |
| 18:20, 17 October 2007 | PyMLWHAM.tgz (file) |  |
58 KB | David Mobley | 1 | |
| 18:28, 17 October 2007 | Amb2gmx.gz (file) | |
8 KB | David Mobley | 1 | |
| 01:04, 29 October 2007 | PyMBAR.tgz (file) | |
66 KB | Michael Shirts | A Python implementation of the MBAR method described in [1]. REFERENCES [1] Shirts MR and Chodera JD. Optimal analysis of multiple equilibrium simulations. Submitted, 2007 | 1 |
| 13:05, 18 May 2011 | README.pdf (file) |  |
77 KB | Michael Shirts | READ ME description of the benchmark system example files | 1 |
| 10:36, 28 August 2011 | Energy comparisons.tgz (file) | |
194 KB | Michael Shirts | cleaned up anthracene test case | 4 |
| 10:39, 28 August 2011 | GROMACS.tgz (file) | |
29.06 MB | Michael Shirts | cleaned up anthracene test case | 2 |
| 10:40, 28 August 2011 | AMBER.tgz (file) | |
15.54 MB | Michael Shirts | Cleaned up anthracene test case | 2 |
| 10:48, 28 August 2011 | DESMOND.tgz (file) | |
63.87 MB | Michael Shirts | cleaned up anthracene test case | 2 |
| 08:45, 13 September 2012 | Transformation small.png (file) |  |
92 KB | Lnaden | Trying to see if I can get a transparent background | 2 |
| 09:46, 13 September 2012 | Ambox notice.png (file) |  |
3 KB | Lnaden | 1 | |
| 15:52, 19 September 2012 | Both topologies.png (file) |  |
163 KB | Lnaden | Image showing a sample of both topology layouts. | 1 |
| 16:54, 19 September 2012 | Linear LJ transformation.png (file) |  |
41 KB | Lnaden | Mediawiki is flipping out apperntly | 4 |
| 15:12, 26 September 2012 | Bind example.png (file) |  |
69 KB | Lnaden | Example image of the binding free energy of ligand A and ligand B | 1 |
| 13:42, 28 September 2012 | Template-info.png (file) |  |
43 KB | Lnaden | 1 | |
| 13:50, 28 September 2012 | Cmbox deletion.png (file) |  |
2 KB | Lnaden | 1 | |
| 12:54, 30 September 2012 | Bootstrap Comparison.png (file) |  |
26 KB | Lnaden | 1 | |
| 12:57, 9 October 2012 | Ethanebox.png (file) |  |
185 KB | Lnaden | Box of TIP3P water molecules and an ethane | 1 |
| 13:38, 9 October 2012 | Phenol.png (file) |  |
39 KB | Lnaden | Phenol, rendered in VMD | 1 |
| 13:39, 9 October 2012 | T4-lysozyme.png (file) |  |
83 KB | Lnaden | T4-lysozyme protein in implicit solvent. Rendered in VMD | 1 |
| 13:40, 9 October 2012 | T4-Phenol.png (file) |  |
89 KB | Lnaden | T4-lysozyme with a Phenol at the binding site, Rendered in VMD | 1 |
| 13:40, 9 October 2012 | T4-Toluene.png (file) |  |
86 KB | Lnaden | T4-lysozyme with a Toluene at the binding site, Rendered in VMD | 1 |
| 13:41, 9 October 2012 | Toluene.png (file) |  |
44 KB | Lnaden | Toluene, Rendered in VMD | 1 |
| 14:53, 9 October 2012 | Doublearrow.png (file) |  |
1 KB | Lnaden | 1 | |
| 08:55, 10 October 2012 | Ethanol.png (file) |  |
23 KB | Lnaden | Ethanol, all atom, rendered in VMD | 1 |
| 08:55, 10 October 2012 | TIP3P-Ethanol.png (file) |  |
178 KB | Lnaden | Ethanol in a TIP3P water box. All atom, rendered in VMD | 1 |
| 08:57, 10 October 2012 | Waterbox.png (file) |  |
174 KB | Lnaden | New water box based on where an ethanol should be instead of ethane. | 2 |
| 09:12, 10 October 2012 | Ethanol in vac.png (file) |  |
4 KB | Lnaden | Ethanol by itself, but the boundary is expanded to show a "box" that it is free to explore. All atom, rendered in VMD | 1 |
| 09:17, 10 October 2012 | Plus sign.jpg (file) |  |
2 KB | Lnaden | Simple plus sign, for use in examples | 1 |
| 09:54, 10 October 2012 | Blackbox.png (file) |  |
1 KB | Lnaden | A nice simple black box, for use in examples | 1 |
| 13:54, 10 October 2012 | Doublearrowupdown.png (file) |  |
1 KB | Lnaden | Double arrow, pointing down and up | 1 |
| 16:37, 10 October 2012 | Toluene Phenol Topology.png (file) |  |
73 KB | Lnaden | 1 | |
| 16:45, 16 October 2012 | TIP3PBox small.png (file) |  |
13 KB | Lnaden | small TIP3PBox with an ethanol cavity. Not equilibrated, rendered in VMD | 1 |
| 16:46, 16 October 2012 | TIP3P-Ethanol small.png (file) |  |
17 KB | Lnaden | Small water box with an ethanol in place. Not equilibrated, rendered in VMD | 1 |
| 16:47, 16 October 2012 | Ethanol in vac small.png (file) |  |
3 KB | Lnaden | Ethanol in a vacuum environment, small picture to better see whats going on. Rendered in VMD | 1 |
| 14:12, 25 October 2012 | Tol-Imp.png (file) |  |
47 KB | Lnaden | Implicit solvent toluene | 1 |
| 14:13, 25 October 2012 | Tol-Nosol.png (file) |  |
40 KB | Lnaden | Toluene up close, again but for tandem use with example | 1 |
| 14:14, 25 October 2012 | T4-Tol-Imp.png (file) |  |
134 KB | Lnaden | T4 Lysozyme and Toluene in an implicit solvent | 1 |
| 14:15, 25 October 2012 | T4-Imp.png (file) |  |
130 KB | Lnaden | T4 in implicit solvent without toluene present | 1 |
| 14:20, 25 October 2012 | Implicit color.png (file) |  |
880 bytes | Lnaden | Empty Implicit Solvent Box | 1 |
| 10:36, 26 October 2012 | T4-Tol-Pull.gif (file) |  |
713 KB | Lnaden | Pulling animation for toluene | 1 |
| 10:57, 26 October 2012 | T4-Tol-Imp-Well.png (file) |  |
135 KB | Lnaden | Added a well to the T4-Toluene system | 1 |
| 16:09, 3 January 2013 | Ethanol.gro (file) | |
182 KB | Michael Shirts | A gro file for ethanol in water. | 1 |
| 16:11, 3 January 2013 | Ethanol.top (file) | |
4 KB | Michael Shirts | Gromacs .top file for Ethanol in TIP3P water parameterized with OPLS-AA | 1 |
| 17:28, 11 July 2013 | Samplecode.png (file) |  |
210 KB | Lnaden | Quick image for sample code used in the How-to box | 1 |
| 07:43, 13 July 2013 | Ligandtranslate.png (file) |  |
20 KB | Michael Shirts | 2 | |
| 12:14, 27 July 2013 | FKBP AMBER GAFF.tgz (file) | |
5.29 MB | Michael Shirts | Input files for ligands LG2,LG3, LG5, LG8, LG9, L12, L14, L20 bound to FKBP. | 1 |
| 17:29, 26 September 2013 | Ethanol.mdp (file) | |
5 KB | Michael Shirts | Changed soft core parameters to default to good ones for single precision. | 3 |
| 17:33, 26 September 2013 | Expanded.mdp (file) | |
6 KB | Michael Shirts | Made the single precision soft core parameters the default. | 7 |
| 15:44, 22 December 2013 | Hamiltonian-exchange-reduced-potential.png (file) |  |
51 KB | John Chodera | 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 |
