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Showing below up to 250 results in range #1 to #250.

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1. A guide to using SLURM to run GPU jobs on pat
2. A guide to using SLURM to run PATHSAMPLE
3. Adding a model for PATHSAMPLE
4. Adding a model to GMIN
5. Adding a model to OPTIM
6. Adding partially finished OPTIM stationary points to a PATHSAMPLE database
7. Adding several minima obtained using GMIN (maybe using BHPT) to min.data
8. Advanced colouring
9. Allowing read access to your directories
10. Alternatively, making the initial path with PATHSAMPLE itself
11. Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)
12. Amberinterface
13. Angle-axis framework
14. Automatic Rigid Body Grouping
15. Aux2bib
16. BLJ60 example input
17. BLJ60 example setup
18. Backup strategy
19. Bash history searching
20. Bash loop tricks
21. Basic linux commands everyone should know!
22. Beginner's guide to working in Wales group
23. Biomolecules in PATHSAMPLE
24. Biomolecules in the energy landscape framework
25. Blacklisting Compilers
26. Branching and Merging
27. CAMSHIFT
28. CHARMM
29. CHECKSPMUTATE
30. CPMDInput
31. Calculating binding free energy using the FSA method
32. Calculating energy of a conformation
33. Calculating molecular properties
34. Calculating order parameters
35. Calculating rate constants (GT and fastest path)
36. Calculating rate constants (SGT, DGT, and SDGT)
37. CamCASP/Bugs
38. CamCASP/CodeExamples/DirectAccess
39. CamCASP/Notes
40. CamCASP/Programming
41. CamCASP/Programming/5/example1
42. CamCASP/ToDo/Memory
43. CamCASP/ToDo/diskIO
44. CamCasp
45. Chain crossing
46. Cmake interface building
47. Colourdiscon.py
48. Common setup problem : No Frequency Warning
49. Compiler Flags
50. Compiling Wales Group code using CMake
51. Compiling and using GMIN with QUIP
52. Compiling and using OPTIM with QUIP
53. Comprehensive Contents Page
54. Computer Office services
55. Computing CHARMM FF energy using GMIN, MMTSB and CHARMM
56. Computing normal modes in angle-axis
57. Computing values only once
58. Connecting Sub-databases
59. Connecting two minima with a pathway
60. Constructing Free Energy Disconnectivity Graphs
61. Conversion between different data file formats
62. Conversion between different image file formats
63. Converting between '.crd' and '.pdb'
64. Creating mismatched DNA duplex using NAB
65. Creating movies (.mpg) of paths using OPTIM
66. DISCOTRESS
67. DMACRYS interface
68. DMAGMIN setup
69. David's .inputrc file
70. Debugging odd transition states in OPTIM
71. Decoding heat capacity curves
72. Density of states and thermodynamics from energy distributions at different temperatures
73. Differences from Clust
74. Dijkstra test.py
75. DisconnectionDPS
76. ElaborateDiff
77. Ellipsoid.model
78. Ellipsoid.model.xyz
79. Ellipsoid.xyz
80. Evaluating different components of AMBER energy function with SANDER
81. Expanding the kinetic transition network with PATHSAMPLE
82. Expanding the kinetic transition network with PATHSAMPLE (CHARMM)
83. Extractedmin2pdb.py
84. Finding an initial path between two end points (minima)
85. Finding an initial path with OPTIM and starting up PATHSAMPLE
86. Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)
87. Finding bugs in latex documents that will not compile
88. Fine tuning UNTRAP
89. Fixing thunderbird links
90. GMIN
91. GMIN MOVES module
92. GMIN SANITY module
93. GMIN TESTS module
94. GenCoords
95. GenCoords Models
96. Gencoords
97. Generating a GMIN Eclipse project
98. Generating parameters using AMBER's built in General Forcefield (gaff)
99. Generating parameters using RESP charges from GAMESS-US
100. Generating pdb, crd and psf for a peptide sequence
101. Getting started with SLURM
102. Git Workflow
103. Global optimization of biomolecules using AMBER9
104. Global optimization of biomolecules using AMBER9 with Structural Restraints
105. Global optimization of biomolecules using CHARMM
106. Gnuplot
107. IMPORTANT: Using PATHSAMPLE safely on sinister
108. Identifying job on a node
109. Identifying the k fastest paths between endpoints using KSHORTESTPATHS
110. If things go wrong...
111. If you lost file min.data, but still you have points.min
112. If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)
113. Installing GROMACS on Clust
114. Installing and setting up the MMTSB toolset
115. Installing packages on your managed CUC3 workstation
116. Installing python modules
117. Instanton tunneling and classical rate calculations with OPTIM
118. Intel Trace Analyzer and Collector
119. Interactive jobs on cluster
120. Jenkins CI
121. Keywords
122. LDAP plans
123. Lapack compilation
124. Latex2html
125. Ligand binding-mode searches with HBONDMATRIX
126. Linear and non-linear regression in gnuplot
127. List of output files for PATHSAMPLE
128. Loading AMBER prmtop and inpcrd files into Pymol
129. Loading OPTIM's min.data.info files into PATHSAMPLE
130. Loading coordinate files into VMD with the help of an AMBER topology file
131. Local Rigid Body Framework
132. Local rigid body in OPTIM
133. MMTSB-toolset
134. Main Page
135. Makerestart
136. Managing interactive jobs on cluster
137. Maui compilation
138. Mek-quake Queueing system
139. Mek-quake initial setup notes
140. Mercurial
141. Migrating to the new SVN server
142. Minimizing a structure using OPTIM and AMBER9
143. Minimizing a structure using OPTIM and CHARMM
144. Mounting sharedscratch locally
145. Mutational BH steps
146. NECI Parallelization
147. New mek-quake
148. No Frequency Warning
149. Notes on AMBER 12 interface
150. Notes on MINPERMDIST
151. OPTIM
152. OPTIM/Q-Chem Tutorial
153. OPTIM and PY ellipsoids tutorial
154. OPTIM output files
155. Optimising a path
156. Optimization tricks
157. Other IT stuff
158. PATHSAMPLE
159. PYGMIN & DMACRYS
160. Parameter-scanning script
161. Path.info file is not read, causes PATHSAMPLE to die
162. Path2pdb.py
163. Path2xyz.py
164. Pathsampling short paths
165. Pathsampling short paths (CHARMM)
166. Pathway Gap Filling Post-CHECKSPMUTATE
167. Pdb to movie.py
168. Pele
169. Performing a hydrogen-bond analysis
170. Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)
171. Perm-pdb.py
172. Perm-prmtop.py
173. Pgprof
174. Piping and redirecting output from one command or file to another
175. PlotGMINms.tcl
176. Plotting a quick histogram in gnuplot using the raw data
177. Plotting data in real time
178. Porfuncs Documentation
179. Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays
180. Preparing an AMBER topology file for a protein plus ligand system
181. Preparing an AMBER topology file for a protein system
182. Preparing input files for a peptide using AMBER
183. Printing files from the command line using 'lpr'
184. Producing a PDB from a coordinates and topology file
185. Producing sexy ray-traced images
186. Program flow
187. Progress
188. Proposed changes to backup and archiving
189. Pymol
190. Python interface for GMIN/OPTIM
191. Quasi-continuous interpolation for biomolecules
192. Quick guide to awk
193. REMD with AMBER
194. REX (Replica EXchange MD) with the MMTSB-toolset
195. Rama upgrade
196. Recommended bash aliases
197. Relaxing existing minima with new potential and creating new database
198. Relaxing existing transition states with new potential and creating new database
199. Remastering Knoppix
200. Removing an excessive number of files from a directory - when 'rm' just isn't enough
201. Removing minima and transition states from the database
202. Restarting a GMIN run from a dump file
203. Revamping the modules system
204. Rigid body input files for proteins using genrigid-input.py
205. Rotamer moves in AMBER
206. Running GMIN with MD move steps AMBER
207. Running a G\=o model with the AMHGMIN
208. Running a Go model with the AMHGMIN
209. Running an Gaussian03 interfaced OPTIM job
210. Running programs in the background
211. STARTING INITIAL PATH JOBS WITH PATHSAMPLE
212. SVN setup
213. See unpacked nodes
214. Selecting search parameters for GMIN
215. Setting up
216. Setting up (CHARMM)
217. Setting up aliases to quickly log you in to a different machine
218. Short 'awk' examples
219. Short 'sed' examples
220. Simple scripts for LEaP to create topology and coordinate files
221. Simulations using OPEP
222. Sorting a file by multiple columns
223. SuSE 10.1 workstation image
224. SuSE 10.2 workstation image
225. SuSE 10.3 workstation image
226. SuSE 11.1
227. Submitting jobs, interactively or to a cluster queue system
228. Symmetrising AMBER topology files
229. Tardis scheduling policy
230. The effect of calculating less than the maximum number of eigenvalues using ENDHESS n
231. Thomson problem in OPTIM
232. Torque and Maui
233. Transfering files to and from your workstation
234. Upgrading destiny
235. Upgrading sword
236. Uploading non image files to the wiki
237. Useful .vmdrc file
238. Using 'ssh-keygen' to automatically log you into clusters from your workstation
239. Using AMBER 14 on the GPU and compute clusters
240. Using BHINTERP to find minima between two end points
241. Using GMIN and OPTIM with GPUs
242. Using GMIN to generate endpoints
243. Using GMIN to generate endpoints (CHARMM)
244. Using Molfacture to edit molecules and add hydrogens
245. Using VMD to display and manipulate '.pdb' files
246. Using tar and gzip to compress/uncompress files
247. Using the implicit membrane model IMM1
248. VMD
249. VMD script to annotate each frame of a trajectory
250. Victor Ruehle

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