.. _sec-peleParameters: PELE parameters in Pele++ control file ====================================== Parameters ---------- temperature ^^^^^^^^^^^ Parameter: double temperature Use: System temperature Note for developers: Used for the Metropolis criterion Units: K Range: (0, inf) Default value: 1000 Plop info: - Plop control file name: 'temp' - Plop parameter name: liga\_params%temp - Plop default value: 298 numberOfPeleSteps ^^^^^^^^^^^^^^^^^ Parameter: unsigned int numberOfPeleSteps Use: Number of Pele steps to complete the simulation. Note for developers: Used in PeleTask::hasTaskFinished Units: Dimensionless Range: [0, inf) Default value: 1000 Plop info: - Plop control file name: 'steps' - Plop parameter name: steps - Plop default value: - .. _sec-peleParameters-activateMinimumSteps: activateMinimumSteps ^^^^^^^^^^^^^^^^^^^^ Parameter: bool minimumStepsActivated Use: Activates the minimum steps functionality, the explorers will continue running pele steps until all have reached the numberOfPeleSteps. **Only for MPI simulations**. Range: True or False Default value: false. .. _sec-peleParameters-waterPerturbationFrequency: waterPerturbationFrequency ^^^^^^^^^^^^^^^^^^^^^^^^^^ Parameter: unsigned int waterPerturnationFrequency Use: Period to perform water perturbation Note for developers: Used in PeleParameters::isTimeToRunWaterPerturbation Units: Dimensionless (# of steps) Range: [0, inf) Default value: 3 Note: If waterPerturbationFrequency = 0, the water perturbation will never be performed. .. _sec-peleParameters-conformationPerturbationFrequency: conformationPerturbationFrequency ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Parameter: unsigned int conformationPerturbationFrequency Use: Period to perform conformation perturbation Note for developers: Used in PeleParameters::testIsTimeToRunConformationPerturbation Units: Dimensionless (# of steps) Range: [0, inf) Default value: 0 Note: If conformationPerturbationFrequency = 0, the conformation perturbation will never be performed. .. _sec-peleParameters-sideChainPerturbationFrequency: sideChainPerturbationFrequency ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Parameter: unsigned int sideChainPerturbationFrequency Use: Period to perform side chain perturbation Note for developers: Used in PeleParameters::testIsTimeToRunSideChainPerturbation Units: Dimensionless (# of steps) Range: [0, inf) Default value: 2 Note: If sideChainPerturbationFrequency = 0, the side chain perturbation will never be performed. .. _sec-peleParameters-anmFrequency: anmFrequency ^^^^^^^^^^^^ Parameter: unsigned int anmStepFrequency Use: Period to perform ANM Note for developers: Used in PeleParameters::isTimeToRunAnm Units: Dimensionless (# of steps) Range: [0, inf) Default value: 2 Plop info: - Plop control file name: 'anmfre' - Plop parameter name: liga\_params%anmfreq - Plop default value: 0 Note: If anmStepFrequency = 0, the ANM will never be performed. .. _sec-peleParameters-loopClosureFrequency: loopClosureFrequency ^^^^^^^^^^^^^^^^^^^^ Parameter: unsigned int loopClosureStepFrequency Use: Period to perform Loop Closure Note for developers: Used in PeleParameters::isTimeToRunLoopClosure Units: Dimensionless (# of steps) Range: [0, inf) Default value: 1 Note: If loopClosureStepFrequency = 0, the Loop Closure will never be performed. .. _sec-peleParameters-sideChainPerturbationFrequency: sideChainPerturbationFrequency ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Parameter: unsigned int sideChainPerturbationFrequency Use: Period to Side Chain Perturbation Note for developers: Used in PeleParameters::isTimeToRunTheSideChainPerturbation Units: Dimensionless (# of steps) Range: [0, inf) Default value: 2 Note: If sideChainPerturbationFrequency = 0, the Side Chain Perturbation will never be performed. .. _sec-peleParameters-minimizationFrequency: minimizationFrequency ^^^^^^^^^^^^^^^^^^^^^ Parameter: unsigned int constrainedMinimizationStepFrequency Use: Period to perform the constrained minimization (if side chain prediction was not performed in that step) Note for developers: Used in PeleParameters::isTimeToRunTheConstrainedMinimization Units: Dimensionless (# of steps) Range: [0, inf) Default value: 1 Plop info: - Plop control file name: 'mifre' - Plop parameter name: liga\_params%minifreq - Plop default value: 1 Note: If constrainedMinimizationStepFrequency = 0, the constrained minimization will never be performed (unless the side chain prediction happens, in which case a final minimization also happens). .. _sec-peleParameters-sideChainPredictionFrequency: sideChainPredictionFrequency ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Parameter: unsigned int sideChainPredictionFrequency Use: Period to perform the side chain prediction Note for developers: Used in PeleParameters::isTimeToRunSideChainPrediction Units: Dimensionless (# of steps) Range: [0, inf) Default value: 3 Plop info: - Plop control file name: 'spfre' - Plop parameter name: liga\_params%sidefreq - Plop default value: 1 Note: If sideChainPredictionFrequency = 0, the side chain prediction will never be performed. .. _sec-peleParameters-numberOfTopSideSelectedLinks: numberOfTopSideSelectedLinks ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Parameter: unsigned int numberOfTopSideSelectedLinks Use: Number of high energy links added to the Pele regions. Note for developers: Used in TopSideLinksSelection::addTopSideLinksTo. Units: Dimensionless Range: [0, inf) Default value: 0 Plop info: - Plop control file name: 'top\_side' - Plop parameter name: liga\_params%top\_side - Plop default value: 0 .. _sec-peleParameters-topSideRadius: topSideRadius ^^^^^^^^^^^^^ Parameter: double topSideRadius Use: Links within this range from any top side link are also added the Pele regions. Note for developers: Used in TopSideLinksSelection::addTopSideLinksTo. Units: :math:`\AA{}` Range: [0, inf) Default value: 0 Plop info: - Plop control file name: 'top\_clust' - Plop parameter name: liga\_params%top\_clust - Plop default value: 0 .. _sec-peleParameters-minimizationRegionRadius: minimizationRegionRadius ^^^^^^^^^^^^^^^^^^^^^^^^ Parameter: double minimizationRegionRadius Use: Links within this radius from the ligand are added to the minimization Pele region. Make sure the includeInMinimization PELE parameter (:ref:`Minimization `) does not interfere with this parameter. Note for developers: Used in PeleRegions::generate. Units: :math:`\AA{}` Range: [0, inf) Default value: 1000.0 (this default intends to include all side chains in the set of includeInMinimization, in case it is different from the whole set of side chains in the system). Plop info: - Plop control file name: 'mirad' - Plop parameter name: liga\_params%minirad - Plop default value: 0 .. _sec-peleParameters-sideChainPredictionRegionRadius: sideChainPredictionRegionRadius ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Parameter: double sideChainPredictionRegionRadius Use: Links within this radius from the ligand are added to the side chain prediction Pele region. Note for developers: Used in PeleRegions::generate. Units: :math:`\AA{}` Range: [0, inf) Default value: 6.0 Plop info: - Plop control file name: 'sprad' - Plop parameter name: liga\_params%siderad - Plop default value: 0 .. _sec-peleParameters-proximityDistance: proximityDistance ^^^^^^^^^^^^^^^^^ Parameter: double proximityDistance Use: Criterion to decide whether a perturbed atomset (usually a ligand) is close enough to perform ANM, Side Chain Prediction, Minimization and solvent updates. Note for developers: Used in PeleStep::runAnm and PeleStep::relax Units: :math:`\AA{}` Range: [0, inf) Default value: 5.0 (only if activateProximityDetection is true). activateProximityDetection ^^^^^^^^^^^^^^^^^^^^^^^^^^ Parameter: bool proximityDetectionActivated Use: Activates the aforementioned distance criterion to perform ANM, Side Chain Prediction, Minimization and solvent updates. Range: True or False Default value: true. .. _sec-peleParameters-perturbationCOMConstraintConstant: removeBulkMovement ^^^^^^^^^^^^^^^^^^ Parameter: bool removeBulkMovement Use: It removes the bulk movement to keep the Complex in the same area during the whole simulation. Whenever the perturbed atomset is a significant fraction of the whole system, the sum of the perturbation of the atomset and the removal of the bulk movement can lead to an apparent movement of the unperturbed region. To avoid this, set the removeBulkMovement to false. Range: True or False Default value: true. perturbationCOMConstraintConstant ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Parameter: double perturbationCOMConstraintConstant Use: Adds a constraint to the center of mass of the perturbed atom set after the perturbation. This will affect the ANM, Side Chain prediction, and the minimization phases. The constraint will be removed before the Metropolis test. Range: [0, inf) Units: :math:`\text{kcal}/(\text{mol} \cdot \AA{}^{2})` Default value: 0 Plop info: - Plop control file name: 'lcom\_con' - Plop parameter name: liga\_params%liga\_com\_constraint - Plop default value: 0 Note: In plop, the atoms are constrained to the COM, so the energy increases when the constraint is addeed. By contrast, we constrain the backbone atoms to their position when the constraint is added, so the energy increases just when the perturbed backbone is moved.