PELESimulation command

Contents:

• PeleSimulation block in PELE++
  • commandType
  • Algorithms
  • RandomGenerator
  • selectionToPerturb
  • NonBonding
  • Pele_parameters
  • Pele_Output
  • Constraints
  • PeleTasks
• PELE output parameters in Pele++ control file
  • Output options and parameters.
  • Example
  • Simulations using MPI
• PELE parameters in Pele++ control file
  • Parameters
• PeleTasks
  • Contents:
  • Constraints
  • metrics
  • jumpif/jumpController block
  • parametersChanges
  • exitCondition
• Random Generator in Pele++ control file
  • Example using a seed
  • Example using a previous random generator stored in a file
• NonBonding in Pele++ control file
  • NonBonding v2 algorithm
  • NonBonding multiscale algorithm
• Perturbation Block in Pele++ control file
  • Example
  • How perturbation of the ligand works
  • How to do Protein-Protein perturbation
  • Steering
  • Perturbation selection
  • Parameters
  • Boxes
• Side Chain Perturbation Block in Pele++ control file
  • Example
  • How side chain perturbation of the ligand works
  • Parameters
• Water Perturbation Block in Pele++ control file
  • Example
  • Global selection of waters to perturb
  • Global box
  • waterSites
  • Parameters
• Conformation Perturbation Block in Pele++ control file
  • Conformation libraries
  • Example
  • Parameters
• ANM Block in Pele++ control file
  • Location
  • Algorithm selection
  • Nodes selection
  • Modes computation
  • Options
  • Parameters
  • linksToInclude
  • linksToOmit
  • anmMinimizer
• Treatment of eigenvector and eigenvalues by the PELE ANM module
• Loop Closure Block in Pele++ control file
  • Location
  • Loop selection
  • Parameters
  • loopClosureMinimizer
• SideChainPrediction Block in Pele++ control file
  • Algorithm selection
  • Links selection
  • Parameters
  • sideChainMinimizer
• Minimization in Pele++ control file
  • Algorithm selection
  • Selection of links to minimize
  • Parameters
  • Truncated Newton Parameters
• Permanent constraints in Pele++ control file
  • Constraint types
• Sensors Block in Pele++ control file
  • Metrics block in Pele++ control file
  • StateTracker types in Pele++ control file
• Jump Controller in Pele++ control file
  • Example
  • jumpIf section
  • jumpController section
  • MPI vs Serial execution
  • Who takes the decisions
  • Jumping (Spawning)
• Interaction Restrictions in Pele++ control file
  • Conditions
  • Example1
  • Example2
• Changeable Parameters
• PELE: Dynamic Changes in simulation parameters
• Exit Conditions