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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)

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