Schrödinger Life-Sciences Molecular Dynamics (MD) Workshop

Wednesday, March 14, 2018

09:00 am

Robin Li and Melissa Ma Science Library Training Room, Room 402 Sapp Center for Teaching and Learning, 376 Lomita Drive Map

Sponsored by:
Stanford Libraries and Schrödinger

Description: 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:

  • Why use molecular dynamics?
  • Setting up MD simulations and best practices
  • Analyzing molecular dynamics trajectories
  • Binding-pose metadynamics
When:
Wednesday, March 14, 2018
09:00 am – 01:00 pm
Where:
Robin Li and Melissa Ma Science Library Training Room, Room 402 Sapp Center for Teaching and Learning, 376 Lomita Drive Map
Admission:

Advance registration required.  Attendees limited to current students, faculty, and staff at Stanford.   Please click on "more info" link to register for this session.

Tags:

Class Engineering Science 

Audience:
Faculty/Staff, Students
Contact:
650-725-1059, graceb@stanford.edu
More info:
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