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  1. The effect of calculating less than the maximum number of eigenvalues using ENDHESS n‏‎ (15:04, 14 March 2011)
  2. Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)‏‎ (15:12, 14 March 2011)
  3. Debugging odd transition states in OPTIM‏‎ (15:47, 14 March 2011)
  4. Expanding the kinetic transition network with PATHSAMPLE‏‎ (15:51, 14 March 2011)
  5. Minimizing a structure using OPTIM and AMBER9‏‎ (16:07, 14 March 2011)
  6. List of output files for PATHSAMPLE‏‎ (17:46, 14 March 2011)
  7. Calculating rate constants (GT and fastest path)‏‎ (17:50, 14 March 2011)
  8. Removing minima and transition states from the database‏‎ (17:59, 17 March 2011)
  9. Finding an initial path with OPTIM and starting up PATHSAMPLE‏‎ (13:50, 6 May 2011)
  10. Using GMIN to generate endpoints‏‎ (16:19, 24 May 2011)
  11. Loading OPTIM's min.data.info files into PATHSAMPLE‏‎ (15:28, 26 May 2011)
  12. Setting up‏‎ (12:25, 29 June 2011)
  13. Pathsampling short paths‏‎ (18:34, 9 September 2011)
  14. Optimising a path‏‎ (18:38, 9 September 2011)
  15. Connecting two minima with a pathway‏‎ (18:52, 7 February 2012)
  16. Setting up (CHARMM)‏‎ (15:52, 8 February 2012)
  17. Using GMIN to generate endpoints (CHARMM)‏‎ (15:54, 8 February 2012)
  18. Expanding the kinetic transition network with PATHSAMPLE (CHARMM)‏‎ (18:11, 4 February 2013)
  19. Pathsampling short paths (CHARMM)‏‎ (18:15, 4 February 2013)
  20. Minimizing a structure using OPTIM and CHARMM‏‎ (18:38, 4 February 2013)
  21. OPTIM‏‎ (12:10, 11 September 2013)
  22. Instanton tunneling and classical rate calculations with OPTIM‏‎ (12:19, 11 September 2013)
  23. GMIN‏‎ (12:20, 20 September 2013)
  24. Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)‏‎ (16:21, 13 November 2013)
  25. OPTIM output files‏‎ (13:43, 4 February 2014)
  26. Adding a model to OPTIM‏‎ (13:53, 4 February 2014)
  27. Compiling Wales Group code using CMake‏‎ (16:02, 3 July 2014)
  28. DisconnectionDPS‏‎ (14:36, 27 November 2014)
  29. Creating movies (.mpg) of paths using OPTIM‏‎ (14:04, 10 August 2015)
  30. Finding an initial path between two end points (minima)‏‎ (18:47, 1 February 2016)
  31. BLJ60 example input‏‎ (18:54, 1 February 2016)
  32. Alternatively, making the initial path with PATHSAMPLE itself‏‎ (18:56, 1 February 2016)
  33. Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)‏‎ (18:59, 1 February 2016)
  34. ElaborateDiff‏‎ (17:33, 10 May 2019)
  35. Jenkins CI‏‎ (17:55, 10 May 2019)
  36. Branching and Merging‏‎ (17:57, 10 May 2019)
  37. Cmake interface building‏‎ (17:58, 10 May 2019)
  38. Installing python modules‏‎ (17:58, 10 May 2019)
  39. Revamping the modules system‏‎ (17:59, 10 May 2019)
  40. CHARMM‏‎ (17:59, 10 May 2019)
  41. Running Wales Group software on Windows 7‏‎ (18:04, 10 May 2019)
  42. Pele‏‎ (18:05, 10 May 2019)
  43. Adding a model to GMIN‏‎ (18:06, 10 May 2019)
  44. Selecting search parameters for GMIN‏‎ (18:06, 10 May 2019)
  45. Global optimization of biomolecules using CHARMM‏‎ (18:07, 10 May 2019)
  46. Global optimization of biomolecules using AMBER9‏‎ (18:08, 10 May 2019)
  47. Global optimization of biomolecules using AMBER9 with Structural Restraints‏‎ (18:08, 10 May 2019)
  48. Calculating binding free energy using the FSA method‏‎ (18:09, 10 May 2019)
  49. Restarting a GMIN run from a dump file‏‎ (18:09, 10 May 2019)
  50. Using the implicit membrane model IMM1‏‎ (18:09, 10 May 2019)
  51. Running a Go model with the AMHGMIN‏‎ (18:10, 10 May 2019)
  52. Running a G\=o model with the AMHGMIN‏‎ (18:10, 10 May 2019)
  53. Ligand binding-mode searches with HBONDMATRIX‏‎ (18:11, 10 May 2019)
  54. Compiling and using GMIN with QUIP‏‎ (18:14, 10 May 2019)
  55. Using GMIN and OPTIM with GPUs‏‎ (18:14, 10 May 2019)
  56. Generating a GMIN Eclipse project‏‎ (18:15, 10 May 2019)
  57. Mutational BH steps‏‎ (18:15, 10 May 2019)
  58. Biomolecules in the energy landscape framework‏‎ (18:16, 10 May 2019)
  59. DMAGMIN setup‏‎ (18:17, 10 May 2019)
  60. Keywords‏‎ (18:17, 10 May 2019)
  61. PYGMIN & DMACRYS‏‎ (18:17, 10 May 2019)
  62. Rotamer moves in AMBER‏‎ (18:18, 10 May 2019)
  63. Python interface for GMIN/OPTIM‏‎ (18:18, 10 May 2019)
  64. Makerestart‏‎ (18:19, 10 May 2019)
  65. Progress‏‎ (18:19, 10 May 2019)
  66. Program flow‏‎ (18:20, 10 May 2019)
  67. Amberinterface‏‎ (18:20, 10 May 2019)
  68. GMIN MOVES module‏‎ (18:21, 10 May 2019)
  69. GMIN SANITY module‏‎ (18:22, 10 May 2019)
  70. GMIN TESTS module‏‎ (18:23, 10 May 2019)
  71. CAMSHIFT‏‎ (18:23, 10 May 2019)
  72. Adding partially finished OPTIM stationary points to a PATHSAMPLE database‏‎ (18:24, 10 May 2019)
  73. Perm-pdb.py‏‎ (18:25, 10 May 2019)
  74. Visualising normal modes using VMD and OPTIM‏‎ (18:25, 10 May 2019)
  75. OPTIM/Q-Chem Tutorial‏‎ (18:26, 10 May 2019)
  76. OPTIM and PY ellipsoids tutorial‏‎ (18:26, 10 May 2019)
  77. Compiling and using OPTIM with QUIP‏‎ (18:27, 10 May 2019)
  78. Running an Gaussian03 interfaced OPTIM job‏‎ (18:27, 10 May 2019)
  79. BLJ60 example setup‏‎ (18:27, 10 May 2019)
  80. Thomson problem in OPTIM‏‎ (18:28, 10 May 2019)
  81. Dijkstra test.py‏‎ (10:14, 13 May 2019)
  82. IMPORTANT: Using PATHSAMPLE safely on sinister‏‎ (10:15, 13 May 2019)
  83. Adding a model for PATHSAMPLE‏‎ (10:16, 13 May 2019)
  84. Using BHINTERP to find minima between two end points‏‎ (10:17, 13 May 2019)
  85. Fine tuning UNTRAP‏‎ (10:17, 13 May 2019)
  86. Calculating rate constants (SGT, DGT, and SDGT)‏‎ (10:18, 13 May 2019)
  87. Identifying the k fastest paths between endpoints using KSHORTESTPATHS‏‎ (10:18, 13 May 2019)
  88. Relaxing existing minima with new potential and creating new database‏‎ (10:19, 13 May 2019)
  89. Relaxing existing transition states with new potential and creating new database‏‎ (10:19, 13 May 2019)
  90. If things go wrong...‏‎ (10:19, 13 May 2019)
  91. If you lost file min.data, but still you have points.min‏‎ (10:20, 13 May 2019)
  92. Path.info file is not read, causes PATHSAMPLE to die‏‎ (10:21, 13 May 2019)
  93. When PATHSAMPLE finds a connected path, but using DIJKSTRA 0 fails to find the connected path‏‎ (10:21, 13 May 2019)
  94. Biomolecules in PATHSAMPLE‏‎ (10:21, 13 May 2019)
  95. Notes on MINPERMDIST‏‎ (10:22, 13 May 2019)
  96. Quasi-continuous interpolation for biomolecules‏‎ (10:23, 13 May 2019)
  97. Notes on AMBER 12 interface‏‎ (10:23, 13 May 2019)
  98. Using AMBER 14 on the GPU and compute clusters‏‎ (10:24, 13 May 2019)
  99. Generating parameters using AMBER's built in General Forcefield (gaff)‏‎ (10:24, 13 May 2019)
  100. Generating parameters using RESP charges from GAMESS-US‏‎ (10:25, 13 May 2019)

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