PROFASI  Version 1.5
Related Pages
Here is a list of all related documentation pages:
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\Table of contents
 oInstallation instructions for ProFASi version 1.5
 oNew in PROFASI version 1.5
 oTutorial 1: A half an hour tour of ProFASi
 oTutorial 2: Using the PROFASI settings file
 oTutorial 3: Simulated annealing
 oTutorial 4: Replica-exchange or parallel tempering MC simulations
 oTutorial 5: Simulated tempering
 oBasicMCRun program reference
 oSimAnnealRun program reference
 oParallel tempering with PROFASI
 |oOptions for temperature history
 |\Options peculiar to parallel tempering
 oSimTempRun program reference
 oWang-Landau method with WLRun
 |\Extra options for Wang Landau iterations
 oRegularization: approximating a protein structure
 oMimiqA : A swiss army knife for RMSD calculations
 oExtracting parts of a PDB file
 oCalculating energies of a PROFASI generated PDB/XML file
 oGenerating native contact lists
 oConverting between structure file formats
 oMerging and converting ProFASi histograms with his1dmerge
 oCreating PROFASI style histograms with prf_his1d
 oCreating PROFASI style 2-d histograms with prf_his2d
 oMerging binary data from His2D objects
 oConverting binary conf files to gzipped text and back
 oScripts
 oCommands for the random number generator
 oCommands to set up the population
 oInitial structures in PROFASI simulations
 oXML configuration file for updates
 oSpecifying relative probability of conformation updates
 oCommands for the Monte Carlo
 oOptions for multi-temperature simulations
 oCommands for setting up measurements/Observables
 |oOptions for all observables
 |oAtomDistance
 |oContactMap
 |oRelative Contact Order
 |oNativeness Q parameter
 |oOligoOrient: Relative orientation of adjacent chains in Oligomers.
 |oProteinRMSD : RMSD of arbitrary type.
 |oRMSD over Ramachandran angles
 |oRadius of gyration
 |oRCBin: Secondary structure analysis based on backbone angles
 |\PeriodicObs
 oPROFASI trajectory files
 oGenerating trajectory files
 oRetrace the trajectory of a single replica of a parallel tempering run
 oRestraining simulations with a torsional angle potential
 oSimulations with distance restraints
 oUsing an arbitrary measurement as a restraint
 oConversion factors between PROFASI units and standard units
 oAccepted sequence input format in PROFASI
 oProFASi DOF identifier strings
 oPROFASI's XML structure file format
 oProFASi PDB handling: Selections and Filters
 oXML templates: Auto-generate complex XML nodes from tabular data
 \New in PROFASI version 1.1

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