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About VLMP

  • What is VLMP?
  • Installation
  • First example

Design and Usage

  • Components
  • Simulation
    • Order
  • Simulation Pool
  • VLMP Execution
    • Local Execution
    • HPC Cluster
  • Workflow
  • Experiments

Components

  • Systems
    • backup
    • seed
    • simulationName
  • Units
    • KcalMol_A
    • none
  • Types
    • basic
    • none
  • Ensembles
    • NVT
    • NVTlambda
  • Models
    • CORONAVIRUS
    • ENM
    • FILE
    • HELIX
    • ICOSPHERE
    • IDP
    • KB
    • MADna
    • MAGNETICNP
    • MEMBRANE
    • PARTICLE
    • PROTEIN_IDP_PROTEIN
    • SBCG
    • SIMULATION
    • SOP
    • SPHEREMULTIBLOB
    • STERIC_LAMBDA_SOLVATION
    • WLC
  • ModelOperations
    • alignInertiaMomentAlongVector
    • distributeRandomly
    • rotation
    • setCenterOfMassPosition
    • setContactDistance
    • setParticleLowestPosition
    • setParticlePositions
    • setParticleXYPosition
  • ModelExtensions
    • ACMagneticField
    • AFM
    • LennardJones
    • WCA
    • absortionSurface
    • addBond
    • constantForce
    • constantForceBetweenCentersOfMass
    • constantForceOverCenterOfMass
    • constantTorqueBetweenCentersOfMass
    • constantTorqueOverCenterOfMass
    • constraintCenterOfMassPosition
    • constraintParticlesListPositionLambda
    • constraintParticlesPosition
    • constraintParticlesPositionLambda
    • harmonicBondBetweenCentersOfMass
    • helixBoundaries
    • plates
    • sphericalShell
    • steric
    • surface
    • surfaceMaxForce
    • uniformMagneticField
  • Integrators
    • BBK
    • EulerMaruyama
    • EulerMaruyamaRigidBody
    • EulerMaruyamaRigidBodyPatchesState
    • GFJ
    • MagneticBrownian
    • NVE
  • SimulationSteps
    • 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

Experiments

  • HighThroughputAFM
    • Introduction
    • Setting Up the Experiment
    • Running the Simulations
    • Analyzing the Results
    • Customizing Your Experiment
    • Advanced Usage
    • Conclusion
  • SurfaceUmbrellaSampling
    • Introduction
    • Setting Up the Experiment
    • Running the Simulations
    • Analyzing the Results
    • Customizing Your Experiment
    • Conclusion
    • References

Extending VLMP

  • How to Extend VLMP
  • Install Extension
  • Sharing Your Extension
  • Templates
    • SYSTEM
    • UNITS
    • TYPES
    • ENSEMBLE
    • MODELS
    • MODEL_OPERATIONS
    • MODEL_EXTENSIONS
    • INTEGRATORS
    • SIMULATION_STEPS
VLMP
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© Copyright 2023, Pablo Ibáñez-Freire.

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