Reference ManualΒΆ
Contents:
- General Structure of a control file in Pele++
- Initialization Block in Pele++ control file
- PELESimulation command
- PeleSimulation block in PELE++
- PELE output parameters in Pele++ control file
- PELE parameters in Pele++ control file
- PeleTasks
- Random Generator in Pele++ control file
- NonBonding in Pele++ control file
- Perturbation Block in Pele++ control file
- Side Chain Perturbation Block in Pele++ control file
- Water Perturbation Block in Pele++ control file
- Conformation Perturbation Block in Pele++ control file
- ANM Block in Pele++ control file
- Treatment of eigenvector and eigenvalues by the PELE ANM module
- Loop Closure Block in Pele++ control file
- SideChainPrediction Block in Pele++ control file
- Minimization in Pele++ control file
- Permanent constraints in Pele++ control file
- Sensors Block in Pele++ control file
- Jump Controller in Pele++ control file
- Interaction Restrictions in Pele++ control file
- Changeable Parameters
- PELE: Dynamic Changes in simulation parameters
- Exit Conditions
- Conditions in Pele++ control file
- Selections By Example
- How to run PELE in multicore platforms
- PCA for the perturbation phase of PELE
- Real Time Control of PELE simulations (experimental)
- PELE File Formats
- PELE default parameters
- PELE Error Messages