Argon Module: Part 1

Introduction to VMD and NAMD

Background information

The assignment

Instructions

Plotting the results

Class Discussion Points

Alternative implementation on the HPC

Argon Module: Part 2

Monte Carlo and Molecular Dynamics analysis of a box of argon atoms

Background information

Instructions

Comparing output

Water Module

Prelude: Water dimer

Assignment

Option 1: Molecular dynamics simulation of water

Option 1: Analysis of the results

Option 2: Monte Carlo simulation of water box

Free Energy Perturbation Module

The solvation energy of ethane and methanol

The solvation energy of group IIA cations

Background Article for Group IIA FEP Calculation

Reactive Canonical Monte Carlo

The haber process

Quench dynamics Module

Setting up the calculation

Analysis of the output