Molecular Dynamics

This is a beginner to intermediate level, in-depth workshop for users with no prior experience using Molecular Dynamics tools. Participants will be guided through AMBER and NAMD software for preparing and performing simulations of biomolecular systems, VMD for visualizing trajectories and manipulating PDB files, and Python for analyzing and plotting simulation data. The four sessions consist of: Practical considerations for Molecular Dynamics; Visualizing Structures with VMD; Molecular Dynamics with AMBER and NAMD; and, Analyzing Molecular Dynamics Data with PYTRAJ. We will be using the online programming environment Jupyter for our teaching. 

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