PROFASI  Version 1.5
Table of contents
  1. Installation

  2. Tutorials

    1. Tutorial 1: A half an hour tour of ProFASi
    2. Tutorial 2: Using the PROFASI settings file
    3. Tutorial 3: Simulated annealing
    4. Tutorial 4: Replica-exchange or parallel tempering MC simulations
    5. Tutorial 5: Simulated tempering
  3. PROFASI simulation programs

    1. BasicMCRun program reference
    2. SimAnnealRun program reference
    3. Parallel tempering with PROFASI
    4. SimTempRun program reference
    5. Wang-Landau method with WLRun
  4. Other utility programs in PROFASI

  5. Configuring PROFASI simulations

  6. Monte Carlo "trajectories"

    1. PROFASI trajectory files
    2. Generating trajectory files
    3. extract_snapshot Recover a single snapshot structure from the trajectory file of a simulation
    4. extract_props Post-process trajectory files
    5. Retrace the trajectory of a single replica of a parallel tempering run This is defunct so far in PROFASI 1.5 beta
  7. Simulations with restraints

    1. Restraining simulations with a torsional angle potential
    2. Simulations with distance restraints
    3. Using an arbitrary measurement as a restraint
  8. Miscellaneous

    1. Conversion factors between PROFASI units and standard units
    2. Accepted sequence input format in PROFASI
    3. ProFASi DOF identifier strings
    4. PROFASI's XML structure file format
    5. ProFASi PDB handling: Selections and Filters
    6. XML templates: Auto-generate complex XML nodes from tabular data
    7. New in PROFASI version 1.1 (Partially obsolete)

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2