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

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