Most linked-to pages

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Showing below up to 209 results in range #1 to #209.

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  1. GMIN‏‎ (35 links)
  2. OPTIM‏‎ (32 links)
  3. AMBER‏‎ (30 links)
  4. PATHSAMPLE‏‎ (29 links)
  5. CHARMM‏‎ (15 links)
  6. User:Mp466‏‎ (11 links)
  7. User:Csw34‏‎ (10 links)
  8. User:Ss2029‏‎ (8 links)
  9. DisconnectionDPS‏‎ (7 links)
  10. CamCASP‏‎ (6 links)
  11. VMD‏‎ (6 links)
  12. User:Cen1001‏‎ (6 links)
  13. Setting up‏‎ (6 links)
  14. Pymol‏‎ (6 links)
  15. PY‏‎ (5 links)
  16. Finding an initial path with OPTIM and starting up PATHSAMPLE‏‎ (5 links)
  17. Compiling Wales Group codes using cmake‏‎ (5 links)
  18. Preparing an AMBER topology file for a protein plus ligand system‏‎ (5 links)
  19. GenCoords‏‎ (5 links)
  20. GenCoords Models‏‎ (4 links)
  21. Ellipsoid.model‏‎ (4 links)
  22. A guide to using SLURM to run GPU jobs on pat‏‎ (4 links)
  23. SVN setup‏‎ (4 links)
  24. Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)‏‎ (4 links)
  25. PlotGMINms.tcl‏‎ (4 links)
  26. Symmetrising AMBER topology files‏‎ (3 links)
  27. List of output files for PATHSAMPLE‏‎ (3 links)
  28. Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)‏‎ (3 links)
  29. DMACRYS interface‏‎ (3 links)
  30. Producing sexy ray-traced images‏‎ (3 links)
  31. Connecting two minima with a pathway‏‎ (3 links)
  32. Ellipsoid.model.xyz‏‎ (3 links)
  33. GMIN MOVES module‏‎ (3 links)
  34. Installing and setting up the MMTSB toolset‏‎ (3 links)
  35. Makerestart‏‎ (3 links)
  36. Mutational BH steps‏‎ (3 links)
  37. User:Jss43‏‎ (3 links)
  38. Creating movies (.mpg) of paths using OPTIM‏‎ (3 links)
  39. A guide to using SLURM to run PATHSAMPLE‏‎ (3 links)
  40. Ellipsoid.xyz‏‎ (3 links)
  41. Generating parameters using AMBER's built in General Forcefield (gaff)‏‎ (3 links)
  42. Compiling GMIN using CMAKE‏‎ (3 links)
  43. SuSE 10.1 workstation image‏‎ (3 links)
  44. User:Jmc49‏‎ (3 links)
  45. Conversion between different data file formats‏‎ (3 links)
  46. Wales Group Version control‏‎ (3 links)
  47. Maui compilation‏‎ (3 links)
  48. Compiling GMIN with CHARMM‏‎ (3 links)
  49. Perm-prmtop.py‏‎ (3 links)
  50. Visualising normal modes using VMD and OPTIM‏‎ (3 links)
  51. Conversion between different image file formats‏‎ (3 links)
  52. Converting between '.crd' and '.pdb'‏‎ (3 links)
  53. Jenkins CI‏‎ (3 links)
  54. Pysites.xyz‏‎ (3 links)
  55. Short 'sed' examples‏‎ (3 links)
  56. Submitting jobs, interactively or to a cluster queue system‏‎ (3 links)
  57. Bash loop tricks‏‎ (2 links)
  58. CHECKSPMUTATE‏‎ (2 links)
  59. Colourdiscon.py‏‎ (2 links)
  60. Global optimization of biomolecules using AMBER9‏‎ (2 links)
  61. If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)‏‎ (2 links)
  62. Useful .vmdrc file‏‎ (2 links)
  63. LDAP plans‏‎ (2 links)
  64. Xmgrace‏‎ (2 links)
  65. User:Am592‏‎ (2 links)
  66. Pdb to movie.py‏‎ (2 links)
  67. Plotting a quick histogram in gnuplot using the raw data‏‎ (2 links)
  68. Producing a PDB from a coordinates and topology file‏‎ (2 links)
  69. Quick guide to awk‏‎ (2 links)
  70. Revamping the modules system‏‎ (2 links)
  71. Running programs in the background‏‎ (2 links)
  72. Simple scripts for LEaP to create topology and coordinate files‏‎ (2 links)
  73. Adding a model for PATHSAMPLE‏‎ (2 links)
  74. Adding a model to OPTIM‏‎ (2 links)
  75. Expanding the kinetic transition network with PATHSAMPLE (CHARMM)‏‎ (2 links)
  76. Pathsampling short paths (CHARMM)‏‎ (2 links)
  77. Basic linux commands everyone should know!‏‎ (2 links)
  78. CamCASP/Programming‏‎ (2 links)
  79. GAMESS‏‎ (2 links)
  80. Global optimization of biomolecules using AMBER9 with Structural Restraints‏‎ (2 links)
  81. Tardis scheduling policy‏‎ (2 links)
  82. Installing GROMACS on Clust‏‎ (2 links)
  83. Using 'ssh-keygen' to automatically log you into clusters from your workstation‏‎ (2 links)
  84. MMTSB-toolset‏‎ (2 links)
  85. Mounting sharedscratch locally‏‎ (2 links)
  86. Pele‏‎ (2 links)
  87. Plotting data in real time‏‎ (2 links)
  88. REMD with AMBER‏‎ (2 links)
  89. Rigid body input files for proteins using genrigid-input.py‏‎ (2 links)
  90. Extracting information from a REX simulation‏‎ (2 links)
  91. Simulations using OPEP‏‎ (2 links)
  92. Adding partially finished OPTIM stationary points to a PATHSAMPLE database‏‎ (2 links)
  93. Loading OPTIM's min.data.info files into PATHSAMPLE‏‎ (2 links)
  94. Comprehensive Contents Page‏‎ (2 links)
  95. The effect of calculating less than the maximum number of eigenvalues using ENDHESS n‏‎ (2 links)
  96. Calculating binding free energy using the FSA method‏‎ (2 links)
  97. Connecting Sub-databases‏‎ (2 links)
  98. DMAGMIN setup‏‎ (2 links)
  99. Global optimization of biomolecules using CHARMM‏‎ (2 links)
  100. Using AMBER 14 on the GPU and compute clusters‏‎ (2 links)
  101. Latex2html‏‎ (2 links)
  102. Performing a hydrogen-bond analysis‏‎ (2 links)
  103. Rotamer moves in AMBER‏‎ (2 links)
  104. Locating and extracting structures (pdbs) from a REX simulation‏‎ (2 links)
  105. Sorting a file by multiple columns‏‎ (2 links)
  106. Optimising a path‏‎ (2 links)
  107. DISCOTRESS‏‎ (2 links)
  108. Automatic Rigid Body Grouping‏‎ (2 links)
  109. Biomolecules in PATHSAMPLE‏‎ (2 links)
  110. Calculating energy of a conformation‏‎ (2 links)
  111. Constructing Free Energy Disconnectivity Graphs‏‎ (2 links)
  112. David's .inputrc file‏‎ (2 links)
  113. GMIN SANITY module‏‎ (2 links)
  114. Gnuplot‏‎ (2 links)
  115. Installing packages on your managed CUC3 workstation‏‎ (2 links)
  116. Using GMIN and OPTIM with GPUs‏‎ (2 links)
  117. Wales Group‏‎ (2 links)
  118. PYGMIN & DMACRYS‏‎ (2 links)
  119. Perm-pdb.py‏‎ (2 links)
  120. Progress‏‎ (2 links)
  121. Rama upgrade‏‎ (2 links)
  122. CamCASP/ToDo‏‎ (2 links)
  123. Running GMIN with MD move steps AMBER‏‎ (2 links)
  124. Producing a free energy surface using WHAM‏‎ (2 links)
  125. Calculating rate constants (GT and fastest path)‏‎ (2 links)
  126. Path.info file is not read, causes PATHSAMPLE to die‏‎ (2 links)
  127. Debugging odd transition states in OPTIM‏‎ (2 links)
  128. Aux2bib‏‎ (2 links)
  129. Biomolecules in the energy landscape framework‏‎ (2 links)
  130. CPMD‏‎ (2 links)
  131. Compiling and using GMIN with QUIP‏‎ (2 links)
  132. Decoding heat capacity curves‏‎ (2 links)
  133. Evaluating different components of AMBER energy function with SANDER‏‎ (2 links)
  134. GMIN TESTS module‏‎ (2 links)
  135. Generating parameters using RESP charges from GAMESS-US‏‎ (2 links)
  136. Transfering files to and from your workstation‏‎ (2 links)
  137. Linear and non-linear regression in gnuplot‏‎ (2 links)
  138. New mek-quake‏‎ (2 links)
  139. Parameter-scanning script‏‎ (2 links)
  140. Proposed changes to backup and archiving‏‎ (2 links)
  141. Recommended bash aliases‏‎ (2 links)
  142. User:Vr274‏‎ (2 links)
  143. Restarting a REX simulation and combining the results‏‎ (2 links)
  144. Paramonov-yaliraki‏‎ (2 links)
  145. Calculating rate constants (SGT, DGT, and SDGT)‏‎ (2 links)
  146. Relaxing existing minima with new potential and creating new database‏‎ (2 links)
  147. Instanton tunneling and classical rate calculations with OPTIM‏‎ (2 links)
  148. Setting up (CHARMM)‏‎ (2 links)
  149. Using GMIN to generate endpoints‏‎ (2 links)
  150. Calculating order parameters‏‎ (2 links)
  151. Density of states and thermodynamics from energy distributions at different temperatures‏‎ (2 links)
  152. Extractedmin2pdb.py‏‎ (2 links)
  153. Generating pdb, crd and psf for a peptide sequence‏‎ (2 links)
  154. Upgrading destiny‏‎ (2 links)
  155. Using VMD to display and manipulate '.pdb' files‏‎ (2 links)
  156. Loading AMBER prmtop and inpcrd files into Pymol‏‎ (2 links)
  157. Mek-quake Queueing system‏‎ (2 links)
  158. SVN Page‏‎ (2 links)
  159. Notes on AMBER 12 interface‏‎ (2 links)
  160. Path2pdb.py‏‎ (2 links)
  161. Pgprof‏‎ (2 links)
  162. Preparing an AMBER topology file for a protein system‏‎ (2 links)
  163. Running a REX simulation with CHARMM‏‎ (2 links)
  164. Setting up aliases to quickly log you in to a different machine‏‎ (2 links)
  165. PlotGMINMs.tcl‏‎ (2 links)
  166. Finding an initial path between two end points (minima)‏‎ (2 links)
  167. Relaxing existing transition states with new potential and creating new database‏‎ (2 links)
  168. Minimizing a structure using OPTIM and AMBER9‏‎ (2 links)
  169. Alternatively, making the initial path with PATHSAMPLE itself‏‎ (2 links)
  170. Using GMIN to generate endpoints (CHARMM)‏‎ (2 links)
  171. Backup strategy‏‎ (2 links)
  172. Branching and Merging‏‎ (2 links)
  173. Computer Office services‏‎ (2 links)
  174. Differences from Clust‏‎ (2 links)
  175. Finding bugs in latex documents that will not compile‏‎ (2 links)
  176. Getting started with SLURM‏‎ (2 links)
  177. Identifying job on a node‏‎ (2 links)
  178. Using tar and gzip to compress/uncompress files‏‎ (2 links)
  179. Loading coordinate files into VMD with the help of an AMBER topology file‏‎ (2 links)
  180. Xfig‏‎ (2 links)
  181. Mek-quake initial setup notes‏‎ (2 links)
  182. Path2xyz.py‏‎ (2 links)
  183. Piping and redirecting output from one command or file to another‏‎ (2 links)
  184. CamCASP/Programming/5‏‎ (2 links)
  185. Python interface for GMIN/OPTIM‏‎ (2 links)
  186. Removing an excessive number of files from a directory - when 'rm' just isn't enough‏‎ (2 links)
  187. Short 'awk' examples‏‎ (2 links)
  188. If things go wrong...‏‎ (2 links)
  189. Removing minima and transition states from the database‏‎ (2 links)
  190. Minimizing a structure using OPTIM and CHARMM‏‎ (2 links)
  191. Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)‏‎ (2 links)
  192. Pathsampling short paths‏‎ (2 links)
  193. Advanced colouring‏‎ (2 links)
  194. Bash history searching‏‎ (2 links)
  195. Computing CHARMM FF energy using GMIN, MMTSB and CHARMM‏‎ (2 links)
  196. Dijkstra test.py‏‎ (2 links)
  197. Uploading non image files to the wiki‏‎ (2 links)
  198. Keywords‏‎ (2 links)
  199. Xmakemol‏‎ (2 links)
  200. Mercurial‏‎ (2 links)
  201. Pathway Gap Filling Post-CHECKSPMUTATE‏‎ (2 links)
  202. User:Ajs1‏‎ (2 links)
  203. Printing files from the command line using 'lpr'‏‎ (2 links)
  204. Quasi-continuous interpolation for biomolecules‏‎ (2 links)
  205. User:Hk286‏‎ (2 links)
  206. If you lost file min.data, but still you have points.min‏‎ (2 links)
  207. Using BHINTERP to find minima between two end points‏‎ (2 links)
  208. OPTIM output files‏‎ (2 links)
  209. Expanding the kinetic transition network with PATHSAMPLE‏‎ (2 links)

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