Most linked-to pages

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

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