Table of contents

1. Installation

   • Installation instructions for ProFASi version 1.5
   • New in PROFASI version 1.5

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

   • Regularization: approximating a protein structure
   • minimize Minimize an expression over degrees of freedom of a protein molecule
   • MimiqA : A swiss army knife for RMSD calculations A command line RMSD tool
   • Extracting parts of a PDB file Retrieve portions of a pdb file.
   • Calculating energies of a PROFASI generated PDB/XML file PROFASI energy terms for a pdb or xml file
   • Generating native contact lists
   • Converting between structure file formats Converting between supported structure file formats
   • Merging and converting ProFASi histograms with his1dmerge Merging histogram data from different compute nodes
   • Creating PROFASI style histograms with prf_his1d Make histograms out of data streams
   • Creating PROFASI style 2-d histograms with prf_his2d Make 2-d histograms out of data streams
   • Merging binary data from His2D objects Merging binary His2D data for 3D plots
   • Converting binary conf files to gzipped text and back Transferring PROFASI binary configuration files to a different machine. This is no longer needed in PROFASI 1.5. See PROFASI trajectory files
   • Scripts

5. Configuring PROFASI simulations

   • Commands for the random number generator
   • Commands to set up the population
   • Initial structures in PROFASI simulations
   • XML configuration file for updates
   • Specifying relative probability of conformation updates
   • Commands for the Monte Carlo
   • Options for multi-temperature simulations
   • Commands for setting up measurements/Observables

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)