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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)
  101. Simple scripts for LEaP to create topology and coordinate files‏‎ (10:25, 13 May 2019)
  102. Using Molfacture to edit molecules and add hydrogens‏‎ (10:26, 13 May 2019)
  103. Preparing an AMBER topology file for a protein plus ligand system‏‎ (10:27, 13 May 2019)
  104. Producing a PDB from a coordinates and topology file‏‎ (10:29, 13 May 2019)
  105. Running GMIN with MD move steps AMBER‏‎ (10:29, 13 May 2019)
  106. Evaluating different components of AMBER energy function with SANDER‏‎ (10:30, 13 May 2019)
  107. REMD with AMBER‏‎ (10:30, 13 May 2019)
  108. Performing a hydrogen-bond analysis‏‎ (10:31, 13 May 2019)
  109. Perm-prmtop.py‏‎ (10:31, 13 May 2019)
  110. Aux2bib‏‎ (10:32, 13 May 2019)
  111. CamCasp‏‎ (10:32, 13 May 2019)
  112. CamCASP/Programming‏‎ (11:27, 13 May 2019)
  113. CamCASP/Programming/5/example1‏‎ (11:28, 13 May 2019)
  114. CamCASP/Notes‏‎ (11:28, 13 May 2019)
  115. CamCASP/Bugs‏‎ (11:29, 13 May 2019)
  116. CamCASP/ToDo/diskIO‏‎ (11:29, 13 May 2019)
  117. CamCASP/ToDo/Memory‏‎ (11:30, 13 May 2019)
  118. CamCASP/CodeExamples/DirectAccess‏‎ (11:30, 13 May 2019)
  119. CPMDInput‏‎ (11:30, 13 May 2019)
  120. Generating pdb, crd and psf for a peptide sequence‏‎ (11:31, 13 May 2019)
  121. Converting between '.crd' and '.pdb'‏‎ (11:32, 13 May 2019)
  122. Calculating energy of a conformation‏‎ (11:32, 13 May 2019)
  123. Calculating molecular properties‏‎ (11:33, 13 May 2019)
  124. Calculating order parameters‏‎ (11:33, 13 May 2019)
  125. If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)‏‎ (11:34, 13 May 2019)
  126. Constructing Free Energy Disconnectivity Graphs‏‎ (11:35, 13 May 2019)
  127. DMACRYS interface‏‎ (11:35, 13 May 2019)
  128. Gnuplot‏‎ (11:36, 13 May 2019)
  129. Plotting a quick histogram in gnuplot using the raw data‏‎ (11:37, 13 May 2019)
  130. Plotting data in real time‏‎ (11:37, 13 May 2019)
  131. Linear and non-linear regression in gnuplot‏‎ (11:38, 13 May 2019)
  132. Installing GROMACS on Clust‏‎ (11:38, 13 May 2019)
  133. Latex2html‏‎ (11:39, 13 May 2019)
  134. MMTSB-toolset‏‎ (11:40, 13 May 2019)
  135. Installing and setting up the MMTSB toolset‏‎ (11:52, 13 May 2019)
  136. REX (Replica EXchange MD) with the MMTSB-toolset‏‎ (11:53, 13 May 2019)
  137. Simulations using OPEP‏‎ (11:53, 13 May 2019)
  138. Pgprof‏‎ (11:54, 13 May 2019)
  139. Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays‏‎ (11:54, 13 May 2019)
  140. Pymol‏‎ (11:55, 13 May 2019)
  141. Loading AMBER prmtop and inpcrd files into Pymol‏‎ (11:55, 13 May 2019)
  142. Producing sexy ray-traced images‏‎ (11:56, 13 May 2019)
  143. Advanced colouring‏‎ (11:57, 13 May 2019)
  144. Path2pdb.py‏‎ (11:58, 13 May 2019)
  145. Extractedmin2pdb.py‏‎ (11:58, 13 May 2019)
  146. Using VMD to display and manipulate '.pdb' files‏‎ (11:59, 13 May 2019)
  147. Loading coordinate files into VMD with the help of an AMBER topology file‏‎ (12:00, 13 May 2019)
  148. Path2xyz.py‏‎ (12:07, 13 May 2019)
  149. Useful .vmdrc file‏‎ (12:08, 13 May 2019)
  150. PlotGMINms.tcl‏‎ (12:08, 13 May 2019)
  151. VMD script to annotate each frame of a trajectory‏‎ (12:09, 13 May 2019)
  152. Xfig‏‎ (12:09, 13 May 2019)
  153. Xmakemol‏‎ (12:10, 13 May 2019)
  154. Xmgrace‏‎ (12:10, 13 May 2019)
  155. Density of states and thermodynamics from energy distributions at different temperatures‏‎ (12:11, 13 May 2019)
  156. Ellipsoid.model‏‎ (12:11, 13 May 2019)
  157. Ellipsoid.model.xyz‏‎ (12:12, 13 May 2019)
  158. Ellipsoid.xyz‏‎ (12:13, 13 May 2019)
  159. Gencoords‏‎ (12:13, 13 May 2019)
  160. GenCoords‏‎ (12:13, 13 May 2019)
  161. GenCoords Models‏‎ (12:14, 13 May 2019)
  162. Angle-axis framework‏‎ (12:14, 13 May 2019)
  163. Computing normal modes in angle-axis‏‎ (12:15, 13 May 2019)
  164. Automatic Rigid Body Grouping‏‎ (12:15, 13 May 2019)
  165. Rigid body input files for proteins using genrigid-input.py‏‎ (12:16, 13 May 2019)
  166. Local Rigid Body Framework‏‎ (12:16, 13 May 2019)
  167. Local rigid body in OPTIM‏‎ (12:16, 13 May 2019)
  168. Colourdiscon.py‏‎ (13:16, 13 May 2019)
  169. Pdb to movie.py‏‎ (13:17, 13 May 2019)
  170. Recommended bash aliases‏‎ (13:17, 13 May 2019)
  171. David's .inputrc file‏‎ (13:18, 13 May 2019)
  172. Computing CHARMM FF energy using GMIN, MMTSB and CHARMM‏‎ (13:18, 13 May 2019)
  173. Parameter-scanning script‏‎ (13:19, 13 May 2019)
  174. Backup strategy‏‎ (13:20, 13 May 2019)
  175. Chain crossing‏‎ (13:20, 13 May 2019)
  176. Computer Office services‏‎ (13:21, 13 May 2019)
  177. Computing values only once‏‎ (13:22, 13 May 2019)
  178. Differences from Clust‏‎ (13:22, 13 May 2019)
  179. Fixing thunderbird links‏‎ (13:24, 13 May 2019)
  180. Intel Trace Analyzer and Collector‏‎ (13:24, 13 May 2019)
  181. LDAP plans‏‎ (13:25, 13 May 2019)
  182. Lapack compilation‏‎ (13:25, 13 May 2019)
  183. Mek-quake Queueing system‏‎ (13:26, 13 May 2019)
  184. Mek-quake initial setup notes‏‎ (13:26, 13 May 2019)
  185. New mek-quake‏‎ (13:26, 13 May 2019)
  186. Maui compilation‏‎ (13:27, 13 May 2019)
  187. Torque and Maui‏‎ (13:27, 13 May 2019)
  188. Mercurial‏‎ (13:28, 13 May 2019)
  189. Migrating to the new SVN server‏‎ (13:28, 13 May 2019)
  190. NECI Parallelization‏‎ (13:28, 13 May 2019)
  191. Optimization tricks‏‎ (13:29, 13 May 2019)
  192. Other IT stuff‏‎ (13:29, 13 May 2019)
  193. Porfuncs Documentation‏‎ (13:30, 13 May 2019)
  194. Proposed changes to backup and archiving‏‎ (13:30, 13 May 2019)
  195. Rama upgrade‏‎ (13:31, 13 May 2019)
  196. Remastering Knoppix‏‎ (13:31, 13 May 2019)
  197. See unpacked nodes‏‎ (13:32, 13 May 2019)
  198. Tardis scheduling policy‏‎ (13:32, 13 May 2019)
  199. Zippo Sicortex machine‏‎ (13:33, 13 May 2019)
  200. Basic linux commands everyone should know!‏‎ (13:35, 13 May 2019)
  201. Piping and redirecting output from one command or file to another‏‎ (13:36, 13 May 2019)
  202. Bash loop tricks‏‎ (13:36, 13 May 2019)
  203. Bash history searching‏‎ (13:36, 13 May 2019)
  204. Setting up aliases to quickly log you in to a different machine‏‎ (13:37, 13 May 2019)
  205. Transfering files to and from your workstation‏‎ (13:37, 13 May 2019)
  206. Using 'ssh-keygen' to automatically log you into clusters from your workstation‏‎ (13:38, 13 May 2019)
  207. Mounting sharedscratch locally‏‎ (13:38, 13 May 2019)
  208. Short 'sed' examples‏‎ (13:39, 13 May 2019)
  209. Quick guide to awk‏‎ (13:39, 13 May 2019)
  210. Short 'awk' examples‏‎ (13:40, 13 May 2019)
  211. Sorting a file by multiple columns‏‎ (13:40, 13 May 2019)
  212. Using tar and gzip to compress/uncompress files‏‎ (13:41, 13 May 2019)
  213. Conversion between different data file formats‏‎ (13:42, 13 May 2019)
  214. Conversion between different image file formats‏‎ (13:42, 13 May 2019)
  215. Removing an excessive number of files from a directory - when 'rm' just isn't enough‏‎ (13:42, 13 May 2019)
  216. Submitting jobs, interactively or to a cluster queue system‏‎ (13:43, 13 May 2019)
  217. Identifying job on a node‏‎ (13:43, 13 May 2019)
  218. A guide to using SLURM to run PATHSAMPLE‏‎ (13:44, 13 May 2019)
  219. A guide to using SLURM to run GPU jobs on pat‏‎ (13:44, 13 May 2019)
  220. Installing packages on your managed CUC3 workstation‏‎ (13:45, 13 May 2019)
  221. Running programs in the background‏‎ (13:45, 13 May 2019)
  222. Finding bugs in latex documents that will not compile‏‎ (13:46, 13 May 2019)
  223. Printing files from the command line using 'lpr'‏‎ (13:46, 13 May 2019)
  224. Uploading non image files to the wiki‏‎ (13:46, 13 May 2019)
  225. Compiler Flags‏‎ (13:49, 13 May 2019)
  226. Blacklisting Compilers‏‎ (13:49, 13 May 2019)
  227. Upgrading destiny‏‎ (13:50, 13 May 2019)
  228. Upgrading sword‏‎ (13:50, 13 May 2019)
  229. SuSE 10.1 workstation image‏‎ (13:50, 13 May 2019)
  230. SuSE 10.2 workstation image‏‎ (13:51, 13 May 2019)
  231. SuSE 10.3 workstation image‏‎ (13:52, 13 May 2019)
  232. SuSE 11.1‏‎ (13:52, 13 May 2019)
  233. Victor Ruehle‏‎ (13:58, 13 May 2019)
  234. PATHSAMPLE‏‎ (11:33, 14 May 2019)
  235. Connecting Sub-databases‏‎ (11:42, 17 May 2019)
  236. Wales Group‏‎ (10:26, 3 June 2019)
  237. No Frequency Warning‏‎ (14:40, 18 July 2019)
  238. Common setup problem : No Frequency Warning‏‎ (16:17, 18 July 2019)
  239. SVN setup‏‎ (00:06, 7 January 2020)
  240. Wales Group Version control‏‎ (00:22, 7 January 2020)
  241. Creating mismatched DNA duplex using NAB‏‎ (12:01, 30 January 2020)
  242. Beginner's guide to working in Wales group‏‎ (19:16, 13 April 2020)
  243. Interactive jobs on cluster‏‎ (12:09, 18 May 2020)
  244. Managing interactive jobs on cluster‏‎ (12:20, 18 May 2020)
  245. Getting started with SLURM‏‎ (14:58, 27 May 2020)
  246. Pathway Gap Filling Post-CHECKSPMUTATE‏‎ (14:54, 4 June 2020)
  247. CHECKSPMUTATE‏‎ (10:53, 17 June 2020)
  248. STARTING INITIAL PATH JOBS WITH PATHSAMPLE‏‎ (11:45, 17 November 2020)
  249. Main Page‏‎ (11:58, 1 July 2021)
  250. Preparing an AMBER topology file for a protein system‏‎ (19:18, 19 July 2021)

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