Explore how to perform molecular dynamics simulations of biomolecules
January 25, 27 and 29, 2021 from 1-4 PM
Part I – Introduction to Molecular Dynamics
January 25, 2021 from 1-4PM
Instructor: Denise Koch
- The nuts and bolts of MD simulations
- Learn how MD simulations work
- Explore force fields used for MD and which molecular systems they apply to
Part II – Preparing Molecular Strucures and performing MD Simulations
January 27, 2021 from 1-4PM
Instructor: Ritu Arora
- Learn how to inspect protein structures with PyMOL
- Prepare MD inputs from crystal data with CHARMM-GUI
- Learn how to perform MD simulations with NAMD
Part III – Analyze MD Simulation Results with VMD
January 29, 2021 from 1-4PM
Instructor: Mohamed Aboelnga
- Displaying molecular structures using Visual Molecular Dynamics (VMD)
- Rendering publication-quality figures and creating simulation movies
- Effectively using VMD tools to analyze MD trajectory
- A certificate of completion for this workshop will be provided to participants upon completion of the workshop series.
- Videos of the workshops will be made available to registrants upon request.
- Basic knowledge of the Linux command line is required to follow these workshops. A link to a series of 3 short 20-min training modules on the Linux command line will be provided to registrants prior to this biosimulations workshop series