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  1. Loading coordinate files into VMD with the help of an AMBER topology file
  2. Local rigid body in OPTIM
  3. Managing interactive jobs on cluster
  4. Maui compilation
  5. Mercurial
  6. Migrating to the new SVN server
  7. Minimizing a structure using OPTIM and AMBER9
  8. Minimizing a structure using OPTIM and CHARMM
  9. Mounting sharedscratch locally
  10. Mutational BH steps
  11. No Frequency Warning
  12. Notes on AMBER 12 interface
  13. Notes on MINPERMDIST
  14. OPTIM/Q-Chem Tutorial
  15. OPTIM output files
  16. Optimization tricks
  17. PYGMIN & DMACRYS
  18. Parameter-scanning script
  19. Path.info file is not read, causes PATHSAMPLE to die
  20. Path2pdb.py
  21. Path2xyz.py
  22. Pdb to movie.py
  23. Pele
  24. Perm-prmtop.py
  25. Pgprof
  26. Piping and redirecting output from one command or file to another
  27. Plotting a quick histogram in gnuplot using the raw data
  28. Plotting data in real time
  29. Porfuncs Documentation
  30. Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays
  31. Preparing input files for a peptide using AMBER
  32. Producing sexy ray-traced images
  33. Progress
  34. Proposed changes to backup and archiving
  35. Python interface for GMIN/OPTIM
  36. Quasi-continuous interpolation for biomolecules
  37. Quick guide to awk
  38. Rama upgrade
  39. Recommended bash aliases
  40. Remastering Knoppix
  41. Removing an excessive number of files from a directory - when 'rm' just isn't enough
  42. Revamping the modules system
  43. Rigid body input files for proteins using genrigid-input.py
  44. Running GMIN with MD move steps AMBER
  45. Running an Gaussian03 interfaced OPTIM job
  46. Running programs in the background
  47. STARTING INITIAL PATH JOBS WITH PATHSAMPLE
  48. Selecting search parameters for GMIN
  49. Setting up aliases to quickly log you in to a different machine
  50. Short 'awk' examples

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