Molecular Simulation

This repository contains a notebook used for development of MD simulation code, and further algorithmic implementation.

Table of Contents

• 1D_System : Currently a notebook which contains pieces of code to simulate the 1D system as described in Chapter 14 of Frenkel & Smit : Undestanding Molecular Simulations - From Algorithms to Applications

Todo

• Understand how to compute energies from psf and prm files.
• Complete energy computation.
• Complete force calculation functions.
• Validate energy and force calculations using existing software.
• Finish MD simulation using velocity verlet integrator.
• Use the MPI interface to code REMD.
• Solve the Hamiltonian equation in the RENS paper.
• Complete integrator with RENS equation.
• Run the simulation and compare graphs with pre-existing graphs.