Molecular Dynamics Kit

This is the documentation for Molecular Dynamics Kit, a library for coarse-grained simulation of proteins based on a model developed at the Institute of Physics of the Polish Academy of Sciences. Developed during a BSc team project at the University of Warsaw.

Authors:

• Jakub Bednarz

• Jakub Boguta

• Paweł Kopaczyk

• Juliusz Pham

• Jan Urbanek

Project home: Github.

Sections:

• Installation
• Preparation layer
  • Contact map files
  • Sequence files
  • PDB objects and parsing
  • Model
  • Parameter files
• Simulation layer
  • Simulation object
  • Data objects
  • Primitives
  • Simulation variables
  • Forces
  • Kernels
  • Verlet list
  • Coordination stats
  • Physical state object
  • Integrators
  • Hooks
• Utilities
  • Amino acid class
  • Contact type class
  • Pair type class
  • Random number generation
  • Residue type class
  • Topology class
  • Physical unit definitions
• Entire namespace