This workshop is designed to be a practical introduction to the method of molecular dynamics simulations. It is intended for students with no prior knowledge. Students will be guided to using various structure prediction software to model missing protein and RNA segments, AMBER and NAMD software for performing simulations of biomolecular systems, VMD for visualizing trajectories and manipulating PDB files, and Python for analyzing and plotting simulation data. The workshop will be conducted in four two hour long hands-on sessions over two weeks consisting of molecular dynamics basics, visual molecular dynamics, building complex simulation systems and molecular dynamics simulation and analysis.

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