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

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