Moldyne

Molecular dynamics and monte carlo simulator written in julia.

This project is based off of lessons learned from Understanding Molecular Dynamics by Frenkel and Smit, The Art of Molecular Dynamics Simulations by Rapaport, and a Computational Statistical Mechanics course on coursera.

Input

The only input file is a PDB (Protein Data Bank) file with ATOM lines containing the atomic positions (2D or 3D).

Output

Two output text files are generated:

1. .out - summary stats per timestep
2. .xyz - coordinates per timestep; can be loaded into VMD as a trajectory

Dimension

The simulation can run in 2D or 3D mode. Both modes can use the same atomic position files, but 2D mode ignores the third position coordinate.

Dependencies

• Distributions
• Plots
• Printf
• Random
• SpecialFunctions