Welcome to VLMP’s documentation!

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