Table of contents

• RMPCDMD
• Algorithms
  • Quaternion velocity Verlet
  • MPCD
  • Molecular Dynamics
  • Boundary conditions
  • Convenience routines
• Design
  • General principles
  • Storage of cell and particle data
  • Programming language
  • Random numbers
• Install
  • Requirements
  • Building on Linux
  • Building on OS X
  • Building on Windows
  • HDF5
  • Python
• Run the code
  • rmpcdmd run
  • rmpcdmd plot
  • rmpcdmd seeder
  • rmpcdmd timers
  • rmpcdmd values
  • experiments/ directory
• Programs
  • Configuration files
  • single_dimer_pbc
  • chemotactic_cell
  • single_body
  • poiseuille_flow
  • single_sphere_thermo_trap
  • n_colloids_pbc
  • three_bead_enzyme
• Tutorial
  • Introduction
  • Preliminary remarks
  • Literature
  • The MPCD fluid and Molecular Dynamics
  • The dimer nanomotor
  • The Janus nanomotor
• Bibliography