MOlecular Dynamics Over Ip

What is this project for?

MODOI is an implementation of the Birkhoff curve shortening procedure using a technique devised by Schwetlick-Zimmer to compute local geodesics. It is currently implemented in Python using multiprocessing to distribute the computing.

How do I get set up?

• Use Git Repository URL: https://github.com/suttond/modoi.git

Who do I talk to?

• For questions about the project please contact Daniel Sutton (sutton.c.daniel@gmail.com)
• For scientific queries please contact Johannes Zimmer (zimmer@maths.bath.ac.uk)

Components

This software package consists of four modules:

• The Algorithm
• Tutorial
  • Butane Simulation
  • Configuring MODOI for Butane
  • Running the Simulation
• Implementations
  • Local_Simulation Script
• Components
  • SimulationClient Package
    • SimulationClient.SimulationClient Module
    • SimulationClient.CustomBFGS Module
    • SimulationClient.Geometric Module
    • SimulationClient.LinearAlgebra Module
    • SimulationClient.MetricValues Module
  • SimulationPotential Module
  • SimulationServer Module
  • SimulationUtilities Package
    • SimulationUtilities.Communication_Codes Module
    • SimulationUtilities.Configuration_Processing Module
    • SimulationUtilities.Curve Module
    • SimulationUtilities.Extract_States_PDB Module
    • SimulationUtilities.Visualize Module

Index

• Index