SimulationSteps

Simulation Steps are a diverse class of components. By adding simulation steps, we introduce specific operations or calculations to be performed at intervals during the simulation. Through this type of operation, we can perform a wide variety of calculations, such as measuring temperature or pressure. We can also calculate properties of the particles like stress or the forces acting on them. One of the most important uses is to save the state of the simulation at certain intervals. This can be done using the “saveState” component, where we can choose from several formats for the data output:

"simulationSteps":[{
                    "type":"saveState",
                    "parameters":{"intervalStep":10000,
                                  "outputFilePath":"output",
                                  "outputFormat":"dcd"}
                                  }
                   ]

The complete list of available simulation steps is as follows:

• AFMMaxForce

• afmMeasurement

• anglesMeasurement

• centerOfMassMeasurement

• forceBetweenSetsMeasurement

• gyrationRadius

• heightMeasurement

• info

• lambdaActivation

• lambdaCycle

• meanMagnetizationMeasurement

• meanRadius

• meanSquareDisplacement

• nativeContactsMeasurement

• oscillatoryForceMeasurement

• pairwiseForces

• patchPolymersMeasurement

• potentialEnergyMeasurement

• potentialMeasurement

• savePatchyParticlesState

• saveState

• stressMeasurement

• thermodynamicIntegration

• thermodynamicMeasurement

• vqcmMeasurement

• vqcmMeasurementFromMobility

---

AFMMaxForce

author

Pablo Ibáñez-Freire

Implements a maximum force criterion for Atomic Force Microscopy (AFM) simulations.

This step terminates the simulation when a specified maximum force is reached.

Required Parameters

Name	Description	Type	Default
maxForce	The maximum force threshold for terminating the simulation.	float

Example:

{
        "type": "AFMMaxForce",
        "parameters":{
                "maxForce": 1000.0
        }
}

---

afmMeasurement

author

Pablo Ibáñez-Freire

Performs measurements for Atomic Force Microscopy (AFM) simulations, recording force-distance data.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for AFM measurements.	str	afm_measurement.dat

Example:

{
        "type": "afmMeasurement",
        "parameters":{
                "outputFilePath": "afm_data.dat"
        }
}

---

anglesMeasurement

author

Pablo Ibáñez-Freire

Measures angles between specified triplets of particles in the simulation.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for angle measurements.	str	angles.dat

Required Selections

Name	Description	Type
selection	Selection of particle triplets for angle measurement.	list of triplets

Example:

{
        "type": "anglesMeasurement",
        "parameters":{
                "outputFilePath": "angle_data.dat",
                "selection": "model1 forceField ANGLES"
        }
}

---

centerOfMassMeasurement

author

Pablo Ibáñez-Freire

Measures the center of mass of a selected group of particles throughout the simulation.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for center of mass measurements.	str	com.dat

Optional Selections

Name	Description	Type
selection	Selection of particles for center of mass calculation.	list of ids

Example:

{
        "type": "centerOfMassMeasurement",
        "parameters":{
                "outputFilePath": "com_data.dat",
                "selection": "model1 type A B C"
        }
}

---

forceBetweenSetsMeasurement

author

Pablo Palacios-Alonso

Measures the force between two sets of particles in the simulation.

Required Parameters

Name	Description	Type	Default
setName_idList	Dictionary mapping set names to lists of particle IDs.	dict
outputFilePath	Path to the output file for force measurements.	str	force_between_sets.dat

Example:

{
        "type": "forceBetweenSetsMeasurement",
        "parameters":{
                "outputFilePath": "force_data.dat",
                "setName_idList": {'set1': [1, 2, 3], 'set2': [4, 5, 6]}
        }
}

---

gyrationRadius

author

Pablo Ibáñez-Freire

Calculates the radius of gyration for a selected group of particles over time.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for gyration radius measurements.	str	gyration_radius.dat

Optional Selections

Name	Description	Type
selection	Selection of particles for gyration radius calculation.	list of ids

Example:

{
        "type": "gyrationRadius",
        "parameters":{
                "outputFilePath": "gyration_data.dat",
                "selection": "model1 type protein"
        }
}

---

heightMeasurement

author

Pablo Ibáñez-Freire

Measures the height of selected particles, typically used in surface-based simulations.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for height measurements.	str	height.dat

Optional Parameters

Name	Description	Type	Default
particleNumberAverage	Number of particles to average for height calculation.	int	1

Optional Selections

Name	Description	Type
selection	Selection of particles for height measurement.	list of ids

Example:

{
        "type": "heightMeasurement",
        "parameters":{
                "outputFilePath": "height_data.dat",
                "particleNumberAverage": 5,
                "selection": "model1 type surface"
        }
}

---

info

author

Pablo Ibáñez-Freire

Provides basic information about the simulation progress, including current step, estimated remaining time, and mean FPS.

Example:

{
        "type": "info",
        "parameters":
        }
}

---

lambdaActivation

author

Pablo Ibáñez-Freire

Controls the activation of lambda parameter in thermodynamic integration simulations.

Required Parameters

Name	Description	Type	Default
lambdaValues	List of lambda values to use in the simulation.	list of float	[0.0, 1.0]
lambdaValueStep	Step size for changing lambda value.	float	0.1

Example:

{
        "type": "lambdaActivation",
        "parameters":{
                "lambdaValueStep": 0.1,
                "lambdaValues": [0.0, 0.2, 0.4, 0.6, 0.8, 1.0]
        }
}

---

lambdaCycle

author

Pablo Ibáñez-Freire

Implements a cycle of lambda values for enhanced sampling in thermodynamic integration.

Required Parameters

Name	Description	Type	Default
activationStep	Number of steps for each lambda activation phase.	int	1000
pauseStep	Number of steps for pause between lambda changes.	int	100
measureStep	Number of steps for measurement at each lambda value.	int	500
lambdaValues	List of lambda values to cycle through.	list of float	[0.0, 1.0]

Example:

{
        "type": "lambdaCycle",
        "parameters":{
                "activationStep": 1000,
                "measureStep": 500,
                "pauseStep": 100,
                "lambdaValues": [0.0, 0.25, 0.5, 0.75, 1.0]
        }
}

---

meanMagnetizationMeasurement

author

16. Palacios Alonso

Measures the mean magnetization of selected magnetic particles in the system.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for mean magnetization measurements.	str	mean_magnetization.dat

Optional Selections

Name	Description	Type
selection	Selection of magnetic particles for magnetization measurement.	list of ids

Example:

{
        "type": "meanMagnetizationMeasurement",
        "parameters":{
                "outputFilePath": "magnetization_data.dat",
                "selection": "model1 type magnetic"
        }
}

---

meanRadius

author

Pablo Ibáñez-Freire

Calculates the mean radius of selected particles over time.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for mean radius measurements.	str	mean_radius.dat

Optional Selections

Name	Description	Type
selection	Selection of particles for mean radius calculation.	list of ids

Example:

{
        "type": "meanRadius",
        "parameters":{
                "outputFilePath": "radius_data.dat",
                "selection": "model1 type sphere"
        }
}

---

meanSquareDisplacement

author

Pablo Diez-Silva

Calculates the mean square displacement (MSD) of selected particles over time.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for MSD measurements.	str	msd.dat

Optional Selections

Name	Description	Type
selection	Selection of particles for MSD calculation.	list of ids

Example:

{
        "type": "meanSquareDisplacement",
        "parameters":{
                "outputFilePath": "msd_data.dat",
                "selection": "model1 type diffusive"
        }
}

---

nativeContactsMeasurement

author

Pablo Ibáñez-Freire

Measures the native contacts between selected pairs of particles, typically used in protein folding simulations.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for native contacts measurements.	str	native_contacts.dat

Required Selections

Name	Description	Type
selection	Selection of particle pairs for native contacts measurement.	list of pairs

Example:

{
        "type": "nativeContactsMeasurement",
        "parameters":{
                "outputFilePath": "contacts_data.dat",
                "selection": "model1 contacts 1:5 6:10 11:15"
        }
}

---

oscillatoryForceMeasurement

author

Pablo Palacios-Alonso

Performs oscillatory force measurements to study viscoelastic properties of the system.

Required Parameters

Name	Description	Type	Default
fluidDensity	Density of the fluid.	float
outputFilePath	Path to the output file for oscillatory force measurements.	str
id_and_force	Dictionary of particle IDs and corresponding force amplitudes.	dict
hydrodynamicRadius	Hydrodynamic radius of the particles.	float
f	Frequency of the oscillatory force.	float
viscosity	Viscosity of the fluid.	float

Optional Parameters

Name	Description	Type	Default
tolerance	Tolerance for Gaussian kernel. Only used if kernel is ‘Gaussian’.	float	1e-05
memory	Number of previous steps to consider in the solver.	int	15
h	Step size for numerical integration. If 0, it’s computed automatically.	float	0.0
damping	Damping factor for the solver.	float	1e-05
maxNIterations	Maximum number of iterations for the solver.	int	10000
toleranceConvergence	Convergence tolerance for the solver.	float	0.0001
kernel	Kernel function for force calculation. Options: ‘Gaussian’ or ‘Peskin3p’.	str	Peskin3p
printSteps	Number of steps between prints of intermediate results.	int	0
notAcceleratedInterval	Interval of non-accelerated steps in the solver.	int	2

Example:

{
        "type": "oscillatoryForceMeasurement",
        "parameters":{
                "outputFilePath": "oscforce_results.dat",
                "f": 1000000.0,
                "hydrodynamicRadius": 1e-09,
                "viscosity": 0.001,
                "fluidDensity": 1000,
                "kernel": "Gaussian",
                "tolerance": 1e-06,
                "maxNIterations": 20000,
                "toleranceConvergence": 1e-05,
                "memory": 20,
                "damping": 1e-06,
                "notAcceleratedInterval": 3,
                "h": 1e-06,
                "printSteps": 100
        }
}

---

pairwiseForces

author

Pablo Palacios-Alonso

Measures pairwise forces between particles in the simulation.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file where pairwise forces will be written.	str

Example:

{
        "type": "pairwiseForces",
        "parameters":{
                "outputFilePath": "pairwise_forces.dat"
        }
}

---

patchPolymersMeasurement

author

Pablo Ibáñez-Freire

Measures properties of polymers created by dynamic bonded patchy particles, including size and surface bonding.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for polymer measurements.	str
bufferSize	Size of the buffer for measurements.	int
surfaceEnergyThreshold	Energy threshold for determining surface bonding.	float

Optional Selections

Name	Description	Type
selection	Selection of patchy particles to measure.	list of ids

Example:

{
        "type": "patchPolymersMeasurement",
        "parameters":{
                "outputFilePath": "patch_polymers.dat",
                "bufferSize": 1000,
                "surfaceEnergyThreshold": -1.0,
                "selection": "model1 type patchy"
        }
}

---

potentialEnergyMeasurement

author

Pablo Ibáñez-Freire

Measures the potential energy of selected particles or the entire system.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for potential energy measurements.	str

Optional Parameters

Name	Description	Type	Default
potentials	List of potential types to measure. If not specified, all potentials are measured.	list of str

Optional Selections

Name	Description	Type
selection	Selection of particles for potential energy measurement.	list of ids

Example:

{
        "type": "potentialEnergyMeasurement",
        "parameters":{
                "outputFilePath": "potential_energy.dat",
                "potentials": ['LennardJones', 'Coulomb'],
                "selection": "model1 type A"
        }
}

---

potentialMeasurement

author

Pablo Ibáñez-Freire

Measures the potential of individual particles in the simulation.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for potential measurements.	str

Required Selections

Name	Description	Type
selection	Selection of particles for potential measurement.	list of ids

Example:

{
        "type": "potentialMeasurement",
        "parameters":{
                "outputFilePath": "particle_potentials.dat",
                "selection": "model1 type B"
        }
}

---

savePatchyParticlesState

author

Pablo Ibáñez-Freire

Saves the state of patchy particles, including their positions and patch orientations.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for saving the state.	str
outputFormat	Format of the output file (e.g., ‘xyz’, ‘pdb’, ‘dcd’).	str

Optional Parameters

Name	Description	Type	Default
pbc	Whether to apply periodic boundary conditions when saving.	bool	False

Optional Selections

Name	Description	Type
selection	Selection of patchy particles to save.	list of ids

Example:

{
        "type": "savePatchyParticlesState",
        "parameters":{
                "outputFilePath": "patchy_state.xyz",
                "outputFormat": "xyz",
                "pbc": True,
                "selection": "model1 type patchy"
        }
}

---

saveState

author

Pablo Ibáñez-Freire

Saves the current state of the simulation, including particle positions and velocities.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for saving the state.	str
outputFormat	Format of the output file (e.g., ‘xyz’, ‘pdb’, ‘dcd’).	str

Optional Parameters

Name	Description	Type	Default
pbc	Whether to apply periodic boundary conditions when saving.	bool	False

Optional Selections

Name	Description	Type
selection	Selection of particles to save. If not specified, all particles are saved.	list of ids

Example:

{
        "type": "saveState",
        "parameters":{
                "outputFilePath": "simulation_state.pdb",
                "outputFormat": "pdb",
                "pbc": True,
                "selection": "model1 all"
        }
}

---

stressMeasurement

author

Pablo Ibáñez-Freire

Measures the stress tensor of the system.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for stress tensor measurements.	str
radiusCutOff	Radius cutoff for the calculation of atom volumes.	float

Example:

{
        "type": "stressMeasurement",
        "parameters":{
                "outputFilePath": "stress_tensor.dat",
                "radiusCutOff": 2.5
        }
}

---

thermodynamicIntegration

author

Pablo Ibáñez-Freire

Performs thermodynamic integration to calculate free energy differences.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for thermodynamic integration results.	str
stepLambda	Step size for lambda parameter in the integration.	float
lambdaValues	List of lambda values for the integration.	list of float

Example:

{
        "type": "thermodynamicIntegration",
        "parameters":{
                "outputFilePath": "ti_results.dat",
                "stepLambda": 0.1,
                "lambdaValues": [0.0, 0.2, 0.4, 0.6, 0.8, 1.0]
        }
}

---

thermodynamicMeasurement

author

Pablo Ibáñez-Freire

Measures various thermodynamic properties of the system, including energy, temperature, and pressure.

Required Parameters

Name	Description	Type	Default
outputFilePath	Path to the output file for thermodynamic measurements.	str

Optional Selections

Name	Description	Type
selection	Selection of particles for thermodynamic measurements. If not specified, all particles are included.	list of ids

Example:

{
        "type": "thermodynamicMeasurement",
        "parameters":{
                "outputFilePath": "thermo.dat",
                "selection": "model1 all"
        }
}

---

vqcmMeasurement

author

Pablo Palacios-Alonso and Pablo Ibáñez-Freire

Performs Virtual Quartz Crystal Microbalance (VQCM) measurements to study viscoelastic properties of the system.

Required Parameters

Name	Description	Type	Default
fluidDensity	Density of the fluid.	float
outputFilePath	Path to the output file for VQCM measurements.	str
f0	Fundamental frequency of the quartz crystal.	float
hydrodynamicRadius	Hydrodynamic radius of the particles.	float
viscosity	Viscosity of the fluid.	float
overtone	Overtone number for the measurement.	int
vwall	Velocity of the wall.	float

Optional Parameters

Name	Description	Type	Default
tolerance	Tolerance for Gaussian kernel. Only used if kernel is ‘Gaussian’.	float	1e-05
memory	Number of previous steps to consider in the solver.	int	5
h	Step size for numerical integration. If 0, it’s computed automatically.	float	0.0
damping	Damping factor for the solver.	float	1e-05
toleranceConvergence	Convergence tolerance for the solver.	float	0.0001
tetherInteractorNames	List of names for tether interactors.	list of str
printSteps	Number of steps between prints of intermediate results.	int	0
notAcceleratedInterval	Interval of non-accelerated steps in the solver.	int	2
maxNIterations	Maximum number of iterations for the solver.	int	10000
kernel	Kernel function for force calculation. Options: ‘Gaussian’ or ‘Peskin3p’.	str	Peskin3p
resonatorImpedance	Impedance of the resonator. If -1, it’s ignored by UAMMD.	float	-1.0

Example:

{
        "type": "vqcmMeasurement",
        "parameters":{
                "outputFilePath": "vqcm_results.dat",
                "f0": 5000000.0,
                "overtone": 3,
                "hydrodynamicRadius": 1e-09,
                "viscosity": 0.001,
                "vwall": 0.001,
                "fluidDensity": 1000,
                "kernel": "Gaussian",
                "tolerance": 1e-06,
                "maxNIterations": 20000,
                "toleranceConvergence": 1e-05,
                "memory": 10,
                "damping": 1e-06,
                "notAcceleratedInterval": 3,
                "h": 1e-06,
                "resonatorImpedance": 1000000.0,
                "printSteps": 100,
                "tetherInteractorNames": ['tether1', 'tether2']
        }
}

---

vqcmMeasurementFromMobility

author

Pablo Palacios-Alonso

Performs Virtual Quartz Crystal Microbalance (VQCM) measurements from mobility data to study viscoelastic properties of the system.

Required Parameters

Name	Description	Type	Default
fluidDensity	Density of the fluid.	float
outputFilePath	Path to the output file for VQCM measurements.	str
f0	Fundamental frequency of the quartz crystal.	float
hydrodynamicRadius	Hydrodynamic radius of the particles.	float
viscosity	Viscosity of the fluid.	float
overtone	Overtone number for the measurement.	int
vwall	Velocity of the wall.	float

Optional Parameters

Name	Description	Type	Default
tolerance	Tolerance for Gaussian kernel. Only used if kernel is ‘Gaussian’.	float	1e-05
h	Step size for numerical integration. If 0, it’s computed automatically.	float	0.0
kernel	Kernel function for force calculation. Options: ‘Gaussian’ or ‘Peskin3p’.	str	Peskin3p
tetherInteractorNames	List of names for tether interactors.	list of str
resonatorImpedance	Impedance of the resonator. If -1, it’s ignored by UAMMD.	float	-1.0

Example:

{
        "type": "vqcmMeasurementFromMobility",
        "parameters":{
                "outputFilePath": "vqcm_mobility_results.dat",
                "f0": 5000000.0,
                "overtone": 3,
                "hydrodynamicRadius": 1e-09,
                "viscosity": 0.001,
                "vwall": 0.001,
                "fluidDensity": 1000,
                "kernel": "Gaussian",
                "tolerance": 1e-06,
                "h": 1e-06,
                "resonatorImpedance": 1000000.0,
                "tetherInteractorNames": ['tether1', 'tether2']
        }
}