Welcome to UAMMD-structured’s documentation!

About UAMMD-structured

• What is UAMMD-structured and what is not?
• UAMMD-structured compilation and installation
  • Installing from conda (recommended)
  • Installing from source
  • Testing
• First Example

UAMMD-structured Guide

• Simulation
• Execution
• Input
  • Data Entry
  • Input Formats
  • Example
• System
  • Handling Errors
• Global
  • Fundamental
  • Units
  • Types
  • Ensemble
• State
• Integrators
• Topology
  • Structure
  • Force Field
• Simulation Steps

Global Data

• Fundamental
  • None
  • Time
  • DynamicallyBondedPatchyParticles
• Units
  • None
  • KcalMol_A
• Types
  • Basic
  • Polarizable
• Ensemble
  • NVT
  • NVTlambda

Integrators

• Minimization
  • SteepestDescent
• NVE
  • Verlet
• NVT
  • Brownian
  • Langevin
  • DPD
  • SPH
  • BDHIOpenBoundary
  • BDHITriplyPeriodic
  • BDHIDoublyPeriodic
  • FluctuatingHydrodynamics
  • Magnetic
• Special
  • None

Interactors

• Bonds
  • Bond1
  • Bond2
  • Bond3
  • Bond4
• Single
  • External
  • Surface
• NonBonded
  • Short Range
  • Electrostatics
• Set
  • Set1
  • Set2
• Atomic Force Microscopy
  • SphericalTip
  • SphericallyBluntedConicTip

Data Structures

• VerletConditionalListSet

Simulation Steps

• SimulationUtils
  • UtilsStep
  • FlowControl
• SimulationOutput
  • WriteStep
• SimulationMeasures
  • ParticlesListMeasure
  • MechanicalMeasure
  • ThermodynamicMeasure
  • GeometricalMeasure
  • MagneticMeasure
  • ExperimentMeasures

Utilities

• Groups
• Scheduling the components
• Batching

pyUAMMD

• Introduction
• Installation
  • Installing from conda (recommended)
  • Installing from source

Implementation

• Input
• Design
  • Simulation
  • System
  • Global
  • State
  • Integrators
  • Topology
• Extending UAMMD-structured
  • Extending ParticleData
  • Extending Global
  • Extending Interactor
  • Extending Integrator
  • Extending SimulationStep
• Information for developers
  • Github actions

Online Examples

• Online Examples