PeleSimulation block in PELE++

commandType

For a whole PELE simulation, it must be set to:

"commandType": "peleSimulation"

Algorithms

Pele must have the following algorithms defined: Perturbation, ANM, Side Chain Prediction and Minimization. If an algorithm is defined at peleSimulation level it is going to be used throughout the whole simulation, unless it is overriden in a task by defining a new one.

RandomGenerator

For more information, check random generator.

Example

"RandomGenerator": {
    "seed": 100586
}

selectionToPerturb

Selects the ligands to be perturbed in the ligand perturbation. If no perturbation is performed (that is, the Perturbation block is empty), then the selection to perturb is empty for all purposes, and this parameter will be ignored.

If the Perturbation block (Perturbation Block in Pele++ control file) is non-empty (that is, perturbation is active), then you must provide this parameter, since it has no default value.

The selection is done for whole chains.

Example

"selectionToPerturb": {
    "chains": {
        "names": [ "L" ]
    }
}

Perturbation of multiple chains.

This feature does not have complete support in PELE (for example, you cannot use different options for different perturb chains; besides, the steering vector is shared between all perturb chains). By knowing which chain is perturbed at each PELE step (see below), you can change the perturbation parameters using the “parametersChanges” block (see PELEDynamicChangesInSimulationParameters) and a counter-based condition (see example 9 of Conditions).

If you specify more than one chain, then PELE will cycle through them perturbing only one of them at each PELE step. The order in which multiple chains are considered for perturbation is:

  • first, protein chains in the order they appear in the input PDB.

  • second, DNA chains in the order they appear in the input PDB.

  • third, RNA chains in the order they appear in the input PDB.

  • fourth, all other chains (ligands) in the order they appear in the input PDB.

Therefore, if you select chains “L”, “M”, both of ligand type, and “M” appears first in the PDB file, then the first PELE step will perturb chain “M”, next step will perturb chain “L”, the step after that will perturb “M”, and so on.

NonBonding

Configuration of the algorithm for non-bonding energy-related terms calculation.

For more details see NonBonding.

Pele_parameters

Parameters used by the Pele algorithm. They can be defined at PeleSimulation or PeleTask level.

For more details see Pele Parameters.

Pele_Output

Parameters related to the output files generated in the simulation. They must be defined at the PeleSimulation level.

For more details see Pele Output Parameters.

Constraints

Constraints applied in all minimizations during a Pele simulation. Check the Constraints section.

PeleTasks

Serie of tasks that Pele has to carry out before a command (and usually a simulation) is considered to be finished.

For more information check the Pele Tasks section.