PELE default parametersΒΆ
This section shows a complete control file with the default values for all parameters in the control file, in the case of a PELE simulation. When each parameter is explained in the documentation, its default value is provided. This section wants to be a quick reference for all the default values of all parameters.
{
// Complete set of default PELE simulation parameters
"simulationLogPath": "",
"controlFileSavingPath": "",
"Initialization": {
// Either the Complex or MultipleComplex sections must be present
// Here, only the Complex section is shown.
"Complex": {
// There is no default for the Complex files, but, of course,
// the complex must be present. The following is an example:
"files": [{"path": "complex.pdb"}]
},
"fixTrees": true,
"fixChainNames": false,
"allowMissingTerminals": false,
"Solvent": {
// If the Solvent block is not defined, then the default
// solventType is VACUUM.
"solventType": "SGBNP",
"useDebyeLength": true,
// ionicStrength only makes sense if useDebyeLength is true and
// the solvent is different from VACUUM.
"ionicStrength": 0.15
},
"ForceField": "OPLS2005"
},
"commands": [
{
"commandType": "peleSimulation",
// The selectionToPerturb has no default
// It must be the user who identifies the chain to perturb,
// in case there is something to perturb.
// In this example, it corresponds to chain L
"selectionToPerturb": { "chains": { "names": ["L"] } },
"NonBonding": {
"nonBondingVersion": "NB_GEN_MSCALE",
"cutoffList":
[ {"type": "shortNeutrumNeutrum", "value": 10},
{"type": "shortChargedNeutrum", "value": 10},
{"type": "shortChargedCharged", "value": 15},
{"type": "longNeutrumNeutrum", "value": 15},
{"type": "longChargedNeutrum", "value": 20},
{"type": "longChargedCharged", "value": 30}
]
},
// The following is considered for all minimizations done
"includeInMinimization": {"chains": "all"},
"doNotIncludeInMinimization": "empty",
// end of minimization related selections
"PELE_Parameters": {
"temperature": 1000,
"numberOfPeleSteps": 1000,
"anmFrequency": 2,
"minimizationFrequency": 1,
"sideChainPredictionFrequency": 3,
"waterPerturbationFrequency": 3,
"conformationPerturbationFrequency": 0,
// The following only make sense if side chain prediction is used
"numberOfTopSideSelectedLinks": 0,
"topSideRadius": 0,
"sideChainPredictionRegionRadius": 6.0,
// end of side chain prediction related fields
"minimizationRegionRadius": 1000.0,
"activateProximityDetection": true,
// proximityDistance is only considered when activateProximityDetection
// is true
"proximityDistance": 5.0,
// perturbationCOMConstraintConstant only makes sense when
// selectionToPerturb is defined
"perturbationCOMConstraintConstant": 0
},
"PELE_Output": {
// Notice that MPI executions will append the trajectory
// number to the trajectory and report paths.
"savingMode": "savingTrajectory",
"trajectoryPath": "../../trajectory.pdb",
// stepsFolder is only used when savingMode is either
// savingSteps or savingBoth
"stepsFolder": "",
"savingFrequencyForAcceptedSteps": 1,
"reportPath": "../../test_report.txt",
"initialPdbPath": "",
"finalPdbPath": "",
"flushingFrequency": 50,
"controllerEventsLogPath": ""
},
// constrains are needed for some simulations.
// constraints come here. There are no default values for the
// different constraint types
"constraints": [],
// PELE tasks come here.
// If no tasks are included,
// an empty list must be written, as is shown:
// example empty list: "PeleTask": [],
"PeleTasks": [
{
// metrics go here. This is an example for a single task.
"metrics": [
// Only the "rmsd" metric has default values.
// For all metrics, "logIt" is true by default
// In the metrics section, besides metrics,
// also state trackers are allowed, but are not typically used
{
"type": "rmsd",
// tags are optional
// "tag": "rmsd1",
"logIt": true,
// Native has no default, but must be specified:
"Native": { "path": "native.pdb"},
// By default, if no selection is specified,
// all atoms are specified.
// The following example selects chain L:
// "selection": { "chains": { "names": ["L"] } },
"selection": {"chains": "all"},
"doSuperposition": true,
// if not specified, superpositionSelection is the same as in
// selection.
// superpositionSelection is only used when doSuperposition
// is true
// "superpositionSelection": { "chains": { "names": ["L"] } }
"includeHydrogens": false
}
]
}
],
// RandomGenerator can be used to force the same seed every time,
// allowing for reproducibility of results. By default,
// the time is used to generate the seed.
// An example RandomGenerator:
// "RandomGenerator": { "seed": 1234 },
// Perturbation only happens if the perturbation block is present.
"Perturbation": {
"perturbationType": "naive",
"translationDirection": "random",
"translationRangeType": "centered",
"rotationAngles": "nonCoupled",
"parameters": {
// These parameters only make sense for perturbationType naive
"numberOfTrials": 10,
"numberOfStericTrials": 500,
// These parameters only make sense for perturbationType metropolis
"numberOfSteps": 1000,
"temperature": 200000,
// These parameters are common to all perturbationTypes
"atLeastOneSelectedTrial": false,
// maxTrialsForAtLeastOne only makes sense if
// atLeastOneSelectedTrial is true
"maxTrialsForAtLeastOne": 1000,
"rotationScalingFactor": 0.5,
"rotationRangeFactor": 0.25,
"translationRange": 1,
"overlapFactor": 0.6,
"steeringUpdateFrequency": 2,
"gridResolution": 30
// A Box would come here as "Box": {}
}
},
// ConformationPerturbation only happens if the conformation perturbation block is present.
"ConformationPerturbation":{
"parameters":{
"overlapFactor": 0.65
}
}
"ANM": {
"algorithm": "ALPHACARBONS",
// When using "CARTESIANS" as algorithm, a "nodes" selection must be used
// By default, "nodes" selects all atoms (for "CARTESIANS").
// If loading modes from a file, you have to use "preloadedModesIn",
// specifying the file
// "preloadedModesIn": "myfile",
"linksToInclude": { "chains": "everythingButLigands"},
"linksToOmit": "empty",
"options": {
"pickingCase": "RANDOM_MODE",
"definedMode": 1,
"directionGeneration": "random",
"initialDirection": 1.0,
"modesMixingOption": "mixMainModeWithOthersModes",
"moveMagnitudeGeneration": "noRandom",
"elasticNetworkModel": "powerContactModel"
},
"parameters": {
"displacementFactor": 1.0,
"numberOfModes": 6,
"thermalScaling": true,
"cutoff": 12.0,
"bondedConstantForHessian": 0.0,
"decayConstant": 1.0,
"constantForHessian": 1.667,
"steeringForce": 20.0,
"relaxationSpringConstant": 0,
"equilibriumParameter": 0.0,
// A very high frequency effectively means that it should only be
// calculated the first time
"eigenUpdateFrequency": 1000000,
"modesChangeFrequency": 6,
// mainModeWeightForMixModes is only used when
// modesMixingOption is mixMainModeWithOthersModes
"mainModeWeightForMixModes": 0.6,
// exponentialDistanceDecay is only used when
// elasticNetworkModel is set to exponentialNetworkModel
"exponentialDistanceDecay": 5.0
},
"anmMinimizer": {
"algorithm": "TruncatedNewton",
"parameters": {
"EnergyDifference": 1.0,
"MinimumRMS": 0.1,
"MaximumMinimizationIterations": 1,
// The following are Truncated Newton parameters
"MaximumNewtonIterations": 30,
"nonBondingListUpdatedEachMinStep": false,
"alphaUpdated": false,
"sgbUpdated": false,
"iterationsBetweenNBlistLongUpdate": 2
}
}
},
"SideChainPrediction": {
"algorithm": "zhexin",
"selectionToInclude": "empty",
"selectionToOmit": "empty",
"parameters": {
"resolution": 30,
"initialOverlapFactor": 0.75,
"minimalOverlapFactor": 0.7,
"randomize": false,
"discardHighEnergySolutions": false,
"numberOfIterations": 1,
// only in "boltzmann" algorithm.
"temperature": 2000
},
// if no sideChainMinimizer block is present, no minimization is done
"sideChainMinimizer": {
"algorithm": "TruncatedNewton",
"parameters": {
"EnergyDifference": 1.0,
"MinimumRMS": 0.1,
"MaximumMinimizationIterations": 3,
// The following are Truncated Newton parameters
"MaximumNewtonIterations": 65,
"nonBondingListUpdatedEachMinStep": true,
"alphaUpdated": false,
"sgbUpdated": true,
"iterationsBetweenNBlistLongUpdate": 2
}
}
},
"Minimizer": {
"algorithm": "TruncatedNewton",
"parameters": {
"EnergyDifference": 1.0,
"MinimumRMS": 0.1,
"MaximumMinimizationIterations": 3,
// The following are Truncated Newton parameters
"MaximumNewtonIterations": 65,
"nonBondingListUpdatedEachMinStep": true,
"alphaUpdated": false,
"sgbUpdated": true,
"iterationsBetweenNBlistLongUpdate": 2
}
}
}
]
}