Schrodinger Workshop: Life-Sciences Molecular Dynamics (MD)


Date and Time 
November 21, 2019
10:00am to 3:00pm
Robin Li & Melissa Ma Science Library, Room 402, Sapp Center for Teaching and Learning
Event Sponsor 
Stanford University Libraries and Schrodinger

This workshop is designed to enable users to run protein molecular dynamics simulations effectively using best practices. Registration required.  This free workshop is limited to current students, faculty, and staff at Stanford.   Please use your Stanford email address when registering.
We cover basic workflows which include how to build systems appropriate for MD, running MD, basic and advanced trajectory analysis tools, and the architecture and configuration of Desmond input and output files. Finally, we will consider the use of binding-pose metadynamics as an approach for improved pose prediction within the context of a protein:ligand complex. Familiarity with Maestro is recommended. More details on MD can be found at:
Topics to be covered:

  • Why use molecular dynamics?
  • Setting up MD simulations and best practices
  • Analyzing molecular dynamics trajectories
  • Binding-pose metadynamics