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1. (hist) ‎Quasi-continuous interpolation for biomolecules ‎[13 bytes]
2. (hist) ‎Ellipsoid.model.xyz ‎[37 bytes]
3. (hist) ‎Running programs in the background ‎[77 bytes]
4. (hist) ‎Bash loop tricks ‎[115 bytes]
5. (hist) ‎Chain crossing ‎[124 bytes]
6. (hist) ‎CAMSHIFT ‎[125 bytes]
7. (hist) ‎Using tar and gzip to compress/uncompress files ‎[162 bytes]
8. (hist) ‎CamCasp ‎[180 bytes]
9. (hist) ‎Using Molfacture to edit molecules and add hydrogens ‎[185 bytes]
10. (hist) ‎New mek-quake ‎[195 bytes]
11. (hist) ‎SuSE 11.1 ‎[230 bytes]
12. (hist) ‎Differences from Clust ‎[265 bytes]
13. (hist) ‎See unpacked nodes ‎[313 bytes]
14. (hist) ‎Installing packages on your managed CUC3 workstation ‎[320 bytes]
15. (hist) ‎Allowing read access to your directories ‎[339 bytes]
16. (hist) ‎Computer Office services ‎[346 bytes]
17. (hist) ‎Instanton tunneling and classical rate calculations with OPTIM ‎[363 bytes]
18. (hist) ‎Other IT stuff ‎[392 bytes]
19. (hist) ‎Generating parameters using AMBER's built in General Forcefield (gaff) ‎[396 bytes]
20. (hist) ‎Bash history searching ‎[427 bytes]
21. (hist) ‎Finding bugs in latex documents that will not compile ‎[436 bytes]
22. (hist) ‎Producing a PDB from a coordinates and topology file ‎[442 bytes]
23. (hist) ‎CamCASP/Notes ‎[453 bytes]
24. (hist) ‎IMPORTANT: Using PATHSAMPLE safely on sinister ‎[460 bytes]
25. (hist) ‎Fixing thunderbird links ‎[464 bytes]
26. (hist) ‎Perm-pdb.py ‎[469 bytes]
27. (hist) ‎Calculating rate constants (SGT, DGT, and SDGT) ‎[485 bytes]
28. (hist) ‎GMIN TESTS module ‎[492 bytes]
29. (hist) ‎CamCASP/Bugs ‎[493 bytes]
30. (hist) ‎Path.info file is not read, causes PATHSAMPLE to die ‎[520 bytes]
31. (hist) ‎If things go wrong... ‎[522 bytes]
32. (hist) ‎CamCASP/Programming ‎[533 bytes]
33. (hist) ‎David's .inputrc file ‎[587 bytes]
34. (hist) ‎When PATHSAMPLE finds a connected path, but using DIJKSTRA 0 fails to find the connected path ‎[602 bytes]
35. (hist) ‎Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM) ‎[616 bytes]
36. (hist) ‎CamCASP/ToDo/Memory ‎[633 bytes]
37. (hist) ‎Xmakemol ‎[638 bytes]
38. (hist) ‎Minimizing a structure using OPTIM and CHARMM ‎[654 bytes]
39. (hist) ‎Useful .vmdrc file ‎[658 bytes]
40. (hist) ‎If you lost file min.data, but still you have points.min ‎[673 bytes]
41. (hist) ‎Plotting data in real time ‎[675 bytes]
42. (hist) ‎Installing and setting up the MMTSB toolset ‎[676 bytes]
43. (hist) ‎Maui compilation ‎[698 bytes]
44. (hist) ‎PYGMIN & DMACRYS ‎[702 bytes]
45. (hist) ‎Xmgrace ‎[710 bytes]
46. (hist) ‎Gnuplot ‎[718 bytes]
47. (hist) ‎Using 'ssh-keygen' to automatically log you into clusters from your workstation ‎[720 bytes]
48. (hist) ‎Adding partially finished OPTIM stationary points to a PATHSAMPLE database ‎[740 bytes]
49. (hist) ‎PlotGMINms.tcl ‎[762 bytes]
50. (hist) ‎Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays ‎[769 bytes]
51. (hist) ‎Adding a model for PATHSAMPLE ‎[822 bytes]
52. (hist) ‎LDAP plans ‎[825 bytes]
53. (hist) ‎Linear and non-linear regression in gnuplot ‎[827 bytes]
54. (hist) ‎Zippo Sicortex machine ‎[831 bytes]
55. (hist) ‎OPTIM ‎[852 bytes]
56. (hist) ‎Thomson problem in OPTIM ‎[875 bytes]
57. (hist) ‎The effect of calculating less than the maximum number of eigenvalues using ENDHESS n ‎[882 bytes]
58. (hist) ‎Adding a model to GMIN ‎[889 bytes]
59. (hist) ‎Torque and Maui ‎[891 bytes]
60. (hist) ‎Upgrading destiny ‎[898 bytes]
61. (hist) ‎Ellipsoid.model ‎[899 bytes]
62. (hist) ‎Amberinterface ‎[921 bytes]
63. (hist) ‎Piping and redirecting output from one command or file to another ‎[950 bytes]
64. (hist) ‎No Frequency Warning ‎[963 bytes]
65. (hist) ‎Colourdiscon.py ‎[996 bytes]
66. (hist) ‎OPTIM output files ‎[1,012 bytes]
67. (hist) ‎Dijkstra test.py ‎[1,019 bytes]
68. (hist) ‎Angle-axis framework ‎[1,040 bytes]
69. (hist) ‎MMTSB-toolset ‎[1,047 bytes]
70. (hist) ‎REX (Replica EXchange MD) with the MMTSB-toolset ‎[1,047 bytes]
71. (hist) ‎Mek-quake initial setup notes ‎[1,052 bytes]
72. (hist) ‎Conversion between different data file formats ‎[1,056 bytes]
73. (hist) ‎Mounting sharedscratch locally ‎[1,094 bytes]
74. (hist) ‎Loading AMBER prmtop and inpcrd files into Pymol ‎[1,102 bytes]
75. (hist) ‎Loading coordinate files into VMD with the help of an AMBER topology file ‎[1,102 bytes]
76. (hist) ‎Minimizing a structure using OPTIM and AMBER9 ‎[1,112 bytes]
77. (hist) ‎Recommended bash aliases ‎[1,116 bytes]
78. (hist) ‎Common setup problem : No Frequency Warning ‎[1,133 bytes]
79. (hist) ‎Rama upgrade ‎[1,135 bytes]
80. (hist) ‎CamCASP/Programming/5/example1 ‎[1,138 bytes]
81. (hist) ‎Conversion between different image file formats ‎[1,157 bytes]
82. (hist) ‎Identifying job on a node ‎[1,164 bytes]
83. (hist) ‎DMAGMIN setup ‎[1,218 bytes]
84. (hist) ‎Selecting search parameters for GMIN ‎[1,219 bytes]
85. (hist) ‎Removing an excessive number of files from a directory - when 'rm' just isn't enough ‎[1,222 bytes]
86. (hist) ‎Intel Trace Analyzer and Collector ‎[1,225 bytes]
87. (hist) ‎PATHSAMPLE ‎[1,236 bytes]
88. (hist) ‎Sorting a file by multiple columns ‎[1,244 bytes]
89. (hist) ‎Connecting two minima with a pathway ‎[1,255 bytes]
90. (hist) ‎Evaluating different components of AMBER energy function with SANDER ‎[1,300 bytes]
91. (hist) ‎Compiling and using OPTIM with QUIP ‎[1,315 bytes]
92. (hist) ‎Expanding the kinetic transition network with PATHSAMPLE (CHARMM) ‎[1,324 bytes]
93. (hist) ‎Transfering files to and from your workstation ‎[1,341 bytes]
94. (hist) ‎Expanding the kinetic transition network with PATHSAMPLE ‎[1,344 bytes]
95. (hist) ‎Upgrading sword ‎[1,451 bytes]
96. (hist) ‎CHARMM ‎[1,460 bytes]
97. (hist) ‎Using GMIN to generate endpoints ‎[1,469 bytes]
98. (hist) ‎Migrating to the new SVN server ‎[1,532 bytes]
99. (hist) ‎Ellipsoid.xyz ‎[1,544 bytes]
100. (hist) ‎Aux2bib ‎[1,588 bytes]
101. (hist) ‎Python interface for GMIN/OPTIM ‎[1,592 bytes]
102. (hist) ‎Global optimization of biomolecules using AMBER9 with Structural Restraints ‎[1,596 bytes]
103. (hist) ‎Pdb to movie.py ‎[1,658 bytes]
104. (hist) ‎Parameter-scanning script ‎[1,659 bytes]
105. (hist) ‎Pymol ‎[1,668 bytes]
106. (hist) ‎Generating a GMIN Eclipse project ‎[1,679 bytes]
107. (hist) ‎Automatic Rigid Body Grouping ‎[1,682 bytes]
108. (hist) ‎Adding a model to OPTIM ‎[1,685 bytes]
109. (hist) ‎Pgprof ‎[1,723 bytes]
110. (hist) ‎Adding several minima obtained using GMIN (maybe using BHPT) to min.data ‎[1,731 bytes]
111. (hist) ‎Using AMBER 14 on the GPU and compute clusters ‎[1,737 bytes]
112. (hist) ‎Decoding heat capacity curves ‎[1,744 bytes]
113. (hist) ‎Running an Gaussian03 interfaced OPTIM job ‎[1,761 bytes]
114. (hist) ‎Victor Ruehle ‎[1,762 bytes]
115. (hist) ‎Beginner's guide to working in Wales group ‎[1,781 bytes]
116. (hist) ‎Setting up aliases to quickly log you in to a different machine ‎[1,811 bytes]
117. (hist) ‎BLJ60 example setup ‎[1,845 bytes]
118. (hist) ‎BLJ60 example input ‎[1,850 bytes]
119. (hist) ‎Gencoords ‎[1,853 bytes]
120. (hist) ‎Removing minima and transition states from the database ‎[1,964 bytes]
121. (hist) ‎Loading OPTIM's min.data.info files into PATHSAMPLE ‎[2,003 bytes]
122. (hist) ‎Interactive jobs on cluster ‎[2,070 bytes]
123. (hist) ‎Managing interactive jobs on cluster ‎[2,070 bytes]
124. (hist) ‎Debugging odd transition states in OPTIM ‎[2,081 bytes]
125. (hist) ‎Printing files from the command line using 'lpr' ‎[2,086 bytes]
126. (hist) ‎AMBER ‎[2,144 bytes]
127. (hist) ‎Xfig ‎[2,147 bytes]
128. (hist) ‎GenCoords ‎[2,149 bytes]
129. (hist) ‎Porfuncs Documentation ‎[2,197 bytes]
130. (hist) ‎A guide to using SLURM to run PATHSAMPLE ‎[2,209 bytes]
131. (hist) ‎Plotting a quick histogram in gnuplot using the raw data ‎[2,280 bytes]
132. (hist) ‎Finding an initial path between two end points (minima) ‎[2,367 bytes]
133. (hist) ‎SuSE 10.2 workstation image ‎[2,396 bytes]
134. (hist) ‎Uploading non image files to the wiki ‎[2,417 bytes]
135. (hist) ‎Converting between '.crd' and '.pdb' ‎[2,443 bytes]
136. (hist) ‎GMIN SANITY module ‎[2,449 bytes]
137. (hist) ‎CamCASP/CodeExamples/DirectAccess ‎[2,455 bytes]
138. (hist) ‎Keywords ‎[2,559 bytes]
139. (hist) ‎If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing) ‎[2,569 bytes]
140. (hist) ‎Progress ‎[2,600 bytes]
141. (hist) ‎Installing GROMACS on Clust ‎[2,614 bytes]
142. (hist) ‎Density of states and thermodynamics from energy distributions at different temperatures ‎[2,664 bytes]
143. (hist) ‎Main Page ‎[2,692 bytes]
144. (hist) ‎Path2xyz.py ‎[2,706 bytes]
145. (hist) ‎Extractedmin2pdb.py ‎[2,732 bytes]
146. (hist) ‎Perm-prmtop.py ‎[2,753 bytes]
147. (hist) ‎Computing values only once ‎[2,756 bytes]
148. (hist) ‎Optimization tricks ‎[2,756 bytes]
149. (hist) ‎OPTIM/Q-Chem Tutorial ‎[2,783 bytes]
150. (hist) ‎DMACRYS interface ‎[2,786 bytes]
151. (hist) ‎Lapack compilation ‎[2,842 bytes]
152. (hist) ‎Global optimization of biomolecules using AMBER9 ‎[2,870 bytes]
153. (hist) ‎Restarting a GMIN run from a dump file ‎[2,961 bytes]
154. (hist) ‎Simple scripts for LEaP to create topology and coordinate files ‎[2,975 bytes]
155. (hist) ‎Identifying the k fastest paths between endpoints using KSHORTESTPATHS ‎[3,077 bytes]
156. (hist) ‎Alternatively, making the initial path with PATHSAMPLE itself (CHARMM) ‎[3,119 bytes]
157. (hist) ‎Computing normal modes in angle-axis ‎[3,152 bytes]
158. (hist) ‎Proposed changes to backup and archiving ‎[3,179 bytes]
159. (hist) ‎Makerestart ‎[3,187 bytes]
160. (hist) ‎Notes on AMBER 12 interface ‎[3,188 bytes]
161. (hist) ‎Running GMIN with MD move steps AMBER ‎[3,196 bytes]
162. (hist) ‎Mek-quake Queueing system ‎[3,235 bytes]
163. (hist) ‎Local Rigid Body Framework ‎[3,260 bytes]
164. (hist) ‎Advanced colouring ‎[3,310 bytes]
165. (hist) ‎Using VMD to display and manipulate '.pdb' files ‎[3,326 bytes]
166. (hist) ‎Latex2html ‎[3,350 bytes]
167. (hist) ‎Constructing Free Energy Disconnectivity Graphs ‎[3,371 bytes]
168. (hist) ‎Running a Go model with the AMHGMIN ‎[3,460 bytes]
169. (hist) ‎SuSE 10.1 workstation image ‎[3,466 bytes]
170. (hist) ‎VMD ‎[3,484 bytes]
171. (hist) ‎Path2pdb.py ‎[3,511 bytes]
172. (hist) ‎Fine tuning UNTRAP ‎[3,565 bytes]
173. (hist) ‎Rotamer moves in AMBER ‎[3,589 bytes]
174. (hist) ‎Calculating molecular properties ‎[3,684 bytes]
175. (hist) ‎CPMDInput ‎[3,711 bytes]
176. (hist) ‎Remastering Knoppix ‎[3,763 bytes]
177. (hist) ‎CamCASP/ToDo/diskIO ‎[3,785 bytes]
178. (hist) ‎Basic linux commands everyone should know! ‎[3,796 bytes]
179. (hist) ‎Calculating energy of a conformation ‎[3,836 bytes]
180. (hist) ‎DISCOTRESS ‎[3,842 bytes]
181. (hist) ‎Compiling and using GMIN with QUIP ‎[3,876 bytes]
182. (hist) ‎Backup strategy ‎[3,990 bytes]
183. (hist) ‎Mercurial ‎[3,996 bytes]
184. (hist) ‎Using BHINTERP to find minima between two end points ‎[4,070 bytes]
185. (hist) ‎Quick guide to awk ‎[4,095 bytes]
186. (hist) ‎Blacklisting Compilers ‎[4,126 bytes]
187. (hist) ‎Creating mismatched DNA duplex using NAB ‎[4,193 bytes]
188. (hist) ‎Local rigid body in OPTIM ‎[4,201 bytes]
189. (hist) ‎Optimising a path ‎[4,298 bytes]
190. (hist) ‎Using GMIN and OPTIM with GPUs ‎[4,492 bytes]
191. (hist) ‎Submitting jobs, interactively or to a cluster queue system ‎[4,493 bytes]
192. (hist) ‎NECI Parallelization ‎[4,577 bytes]
193. (hist) ‎Running Wales Group software on Windows 7 ‎[4,961 bytes]
194. (hist) ‎Relaxing existing minima with new potential and creating new database ‎[4,970 bytes]
195. (hist) ‎List of output files for PATHSAMPLE ‎[5,015 bytes]
196. (hist) ‎Using the implicit membrane model IMM1 ‎[5,158 bytes]
197. (hist) ‎Running a G\=o model with the AMHGMIN ‎[5,158 bytes]
198. (hist) ‎Preparing an AMBER topology file for a protein system ‎[5,198 bytes]
199. (hist) ‎Relaxing existing transition states with new potential and creating new database ‎[5,210 bytes]
200. (hist) ‎Producing sexy ray-traced images ‎[5,214 bytes]
201. (hist) ‎SuSE 10.3 workstation image ‎[5,291 bytes]
202. (hist) ‎Pele ‎[5,408 bytes]
203. (hist) ‎Performing a hydrogen-bond analysis ‎[5,610 bytes]
204. (hist) ‎Installing python modules ‎[5,638 bytes]
205. (hist) ‎Jenkins CI ‎[5,650 bytes]
206. (hist) ‎A guide to using SLURM to run GPU jobs on pat ‎[5,661 bytes]
207. (hist) ‎Generating parameters using RESP charges from GAMESS-US ‎[5,728 bytes]
208. (hist) ‎Branching and Merging ‎[5,765 bytes]
209. (hist) ‎Biomolecules in the energy landscape framework ‎[5,826 bytes]
210. (hist) ‎Pathsampling short paths ‎[5,889 bytes]
211. (hist) ‎Pathsampling short paths (CHARMM) ‎[5,927 bytes]
212. (hist) ‎GenCoords Models ‎[5,958 bytes]
213. (hist) ‎Using GMIN to generate endpoints (CHARMM) ‎[5,983 bytes]
214. (hist) ‎Creating movies (.mpg) of paths using OPTIM ‎[6,196 bytes]
215. (hist) ‎Simulations using OPEP ‎[6,320 bytes]
216. (hist) ‎GMIN MOVES module ‎[6,446 bytes]
217. (hist) ‎Tardis scheduling policy ‎[6,504 bytes]
218. (hist) ‎Setting up (CHARMM) ‎[6,517 bytes]
219. (hist) ‎Wales Group Version control ‎[6,942 bytes]
220. (hist) ‎Biomolecules in PATHSAMPLE ‎[7,372 bytes]
221. (hist) ‎Alternatively, making the initial path with PATHSAMPLE itself ‎[7,653 bytes]
222. (hist) ‎Compiler Flags ‎[7,696 bytes]
223. (hist) ‎DisconnectionDPS ‎[7,707 bytes]
224. (hist) ‎Symmetrising AMBER topology files ‎[7,778 bytes]
225. (hist) ‎Cmake interface building ‎[7,888 bytes]
226. (hist) ‎VMD script to annotate each frame of a trajectory ‎[8,489 bytes]
227. (hist) ‎Revamping the modules system ‎[9,487 bytes]
228. (hist) ‎STARTING INITIAL PATH JOBS WITH PATHSAMPLE ‎[9,540 bytes]
229. (hist) ‎OPTIM and PY ellipsoids tutorial ‎[9,800 bytes]
230. (hist) ‎Compiling Wales Group code using CMake ‎[10,074 bytes]
231. (hist) ‎Short 'awk' examples ‎[10,094 bytes]
232. (hist) ‎Visualising normal modes using VMD and OPTIM ‎[10,712 bytes]
233. (hist) ‎Mutational BH steps ‎[11,478 bytes]
234. (hist) ‎Wales Group ‎[11,619 bytes]
235. (hist) ‎Calculating order parameters ‎[11,790 bytes]
236. (hist) ‎Ligand binding-mode searches with HBONDMATRIX ‎[11,806 bytes]
237. (hist) ‎Setting up ‎[11,969 bytes]
238. (hist) ‎Finding an initial path with OPTIM and starting up PATHSAMPLE ‎[12,467 bytes]
239. (hist) ‎REMD with AMBER ‎[12,903 bytes]
240. (hist) ‎Generating pdb, crd and psf for a peptide sequence ‎[14,527 bytes]
241. (hist) ‎Calculating rate constants (GT and fastest path) ‎[16,099 bytes]
242. (hist) ‎Global optimization of biomolecules using CHARMM ‎[16,664 bytes]
243. (hist) ‎Notes on MINPERMDIST ‎[17,293 bytes]
244. (hist) ‎SVN setup ‎[17,553 bytes]
245. (hist) ‎Preparing an AMBER topology file for a protein plus ligand system ‎[17,913 bytes]
246. (hist) ‎Preparing input files for a peptide using AMBER ‎[17,945 bytes]
247. (hist) ‎Computing CHARMM FF energy using GMIN, MMTSB and CHARMM ‎[17,962 bytes]
248. (hist) ‎Short 'sed' examples ‎[18,380 bytes]
249. (hist) ‎Compiling Wales Group codes using cmake ‎[18,973 bytes]
250. (hist) ‎ElaborateDiff ‎[19,530 bytes]
251. (hist) ‎Git Workflow ‎[19,580 bytes]
252. (hist) ‎Connecting Sub-databases ‎[19,593 bytes]
253. (hist) ‎Getting started with SLURM ‎[20,194 bytes]
254. (hist) ‎Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM) ‎[20,283 bytes]
255. (hist) ‎Rigid body input files for proteins using genrigid-input.py ‎[20,574 bytes]
256. (hist) ‎CHECKSPMUTATE ‎[21,602 bytes]
257. (hist) ‎Program flow ‎[24,578 bytes]
258. (hist) ‎Comprehensive Contents Page ‎[25,020 bytes]
259. (hist) ‎Pathway Gap Filling Post-CHECKSPMUTATE ‎[26,568 bytes]
260. (hist) ‎GMIN ‎[57,544 bytes]
261. (hist) ‎Calculating binding free energy using the FSA method ‎[58,507 bytes]

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