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1. A guide to using SLURM to run GPU jobs on pat
2. Adding several minima obtained using GMIN (maybe using BHPT) to min.data
3. Allowing read access to your directories
4. Angle-axis framework
5. Aux2bib
6. Backup strategy
7. Bash history searching
8. Bash loop tricks
9. Beginner's guide to working in Wales group
10. Biomolecules in PATHSAMPLE
11. Blacklisting Compilers
12. Branching and Merging
13. Calculating rate constants (SGT, DGT, and SDGT)
14. Chain crossing
15. Cmake interface building
16. Colourdiscon.py
17. Common setup problem : No Frequency Warning
18. Compiler Flags
19. Compiling and using GMIN with QUIP
20. Computer Office services
21. Computing normal modes in angle-axis
22. Computing values only once
23. Constructing Free Energy Disconnectivity Graphs
24. Conversion between different image file formats
25. Creating mismatched DNA duplex using NAB
26. David's .inputrc file
27. Decoding heat capacity curves
28. Differences from Clust
29. Dijkstra test.py
30. Extractedmin2pdb.py
31. Finding bugs in latex documents that will not compile
32. Fixing thunderbird links
33. Generating a GMIN Eclipse project
34. Git Workflow
35. Global optimization of biomolecules using AMBER9
36. Global optimization of biomolecules using AMBER9 with Structural Restraints
37. IMPORTANT: Using PATHSAMPLE safely on sinister
38. Identifying job on a node
39. If things go wrong...
40. If you lost file min.data, but still you have points.min
41. Installing packages on your managed CUC3 workstation
42. Instanton tunneling and classical rate calculations with OPTIM
43. Intel Trace Analyzer and Collector
44. Interactive jobs on cluster
45. Jenkins CI
46. Keywords
47. LDAP plans
48. Latex2html
49. Linear and non-linear regression in gnuplot
50. Loading AMBER prmtop and inpcrd files into Pymol
51. Loading coordinate files into VMD with the help of an AMBER topology file
52. Local rigid body in OPTIM
53. Managing interactive jobs on cluster
54. Maui compilation
55. Mercurial
56. Migrating to the new SVN server
57. Minimizing a structure using OPTIM and AMBER9
58. Minimizing a structure using OPTIM and CHARMM
59. Mounting sharedscratch locally
60. Mutational BH steps
61. No Frequency Warning
62. Notes on AMBER 12 interface
63. Notes on MINPERMDIST
64. OPTIM/Q-Chem Tutorial
65. OPTIM output files
66. Optimization tricks
67. PYGMIN & DMACRYS
68. Parameter-scanning script
69. Path.info file is not read, causes PATHSAMPLE to die
70. Path2pdb.py
71. Path2xyz.py
72. Pdb to movie.py
73. Pele
74. Perm-prmtop.py
75. Pgprof
76. Piping and redirecting output from one command or file to another
77. Plotting a quick histogram in gnuplot using the raw data
78. Plotting data in real time
79. Porfuncs Documentation
80. Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays
81. Preparing input files for a peptide using AMBER
82. Producing sexy ray-traced images
83. Progress
84. Proposed changes to backup and archiving
85. Python interface for GMIN/OPTIM
86. Quasi-continuous interpolation for biomolecules
87. Quick guide to awk
88. Rama upgrade
89. Recommended bash aliases
90. Remastering Knoppix
91. Removing an excessive number of files from a directory - when 'rm' just isn't enough
92. Revamping the modules system
93. Rigid body input files for proteins using genrigid-input.py
94. Running GMIN with MD move steps AMBER
95. Running an Gaussian03 interfaced OPTIM job
96. Running programs in the background
97. STARTING INITIAL PATH JOBS WITH PATHSAMPLE
98. Selecting search parameters for GMIN
99. Setting up aliases to quickly log you in to a different machine
100. Short 'awk' examples

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