Schrödinger Workshop: Life-Sciences Molecular Dynamics

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Date and Time 
January 15, 2019
2:00pm to 6:00pm
Location 
Robin Li and Melissa Ma Science Library, Training Room (Room 402) at 376 Lomita Drive, Sapp Center for Science Teaching and Learning
Admission 

Registration is required and is limited to current students, postdocs, faculty, and staff at Stanford. Please use your @stanford.edu email address when registering.  Click on More Info link to register for this event.

Audience 
Faculty/Staff
Students
Event Sponsor 
Stanford Libraries and Schrödinger
Contact 
graceb@stanford.edu
650-725-1039

This workshop is designed to enable users to run protein molecular dynamics simulations effectively using best practices. 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: https://www.schrodinger.com/desmond
Topics to be covered:1. Why use molecular dynamics? 2. Setting up MD simulations and best practices3. Analyzing molecular dynamics trajectories4. Binding-pose metadynamics

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