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: -

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.

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.

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.

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.

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.

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.

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.

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).

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.

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: \(\AA{}\)

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

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 (Minimization) does not interfere with this parameter.

Note for developers: Used in PeleRegions::generate.

Units: \(\AA{}\)

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

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: \(\AA{}\)

Range: [0, inf)

Default value: 6.0

Plop info:

  • Plop control file name: ‘sprad’

  • Plop parameter name: liga_params%siderad

  • Plop default value: 0

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: \(\AA{}\)

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.

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: \(\text{kcal}/(\text{mol} \cdot \AA{}^{2})\)

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.