PROFASI
Version 1.5
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Modules
Namespaces
Classes
Table of contents
Installation
Installation instructions for ProFASi version 1.5
New in PROFASI version 1.5
Tutorials
Tutorial 1: A half an hour tour of ProFASi
Tutorial 2: Using the PROFASI settings file
Tutorial 3: Simulated annealing
Tutorial 4: Replica-exchange or parallel tempering MC simulations
Tutorial 5: Simulated tempering
PROFASI simulation programs
BasicMCRun program reference
SimAnnealRun program reference
Parallel tempering with PROFASI
SimTempRun program reference
Wang-Landau method with WLRun
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
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
Monte Carlo "trajectories"
PROFASI trajectory files
Generating trajectory files
extract_snapshot
Recover a single snapshot structure from the trajectory file of a simulation
extract_props
Post-process trajectory files
Retrace the trajectory of a single replica of a parallel tempering run
This is defunct so far in PROFASI 1.5 beta
Simulations with restraints
Restraining simulations with a torsional angle potential
Simulations with distance restraints
Using an arbitrary measurement as a restraint
Miscellaneous
Conversion factors between PROFASI units and standard units
Accepted sequence input format in PROFASI
ProFASi DOF identifier strings
PROFASI's XML structure file format
ProFASi PDB handling: Selections and Filters
XML templates: Auto-generate complex XML nodes from tabular data
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