Molecular Dynamics

Wed, Apr 10, 2024 1:00pm - Fri, Apr 19, 2024 4:00pm

Status: Completed

This workshop is designed to be a practical introduction to the method of molecular dynamics simulations.

This is a beginner-to-intermediate level, in-depth workshop for users with no prior experience using Molecular Dynamics tools. However, participants should have some experience working with the command line.

Participants will be guided through preparing systems for AMBER and NAMD software and 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 three-hour hands-on sessions over two weeks.


April 10, 2022, 1:00 - 4:00 pm (Atlantic time): Practical considerations for Molecular Dynamics

April 12, 2022, 1:00 - 4:00 pm (Atlantic time): Visualizing Structures with VMD

April 17, 2022, 1:00 - 4:00 pm (Atlantic time): Molecular Dynamics with AMBER and NAMD

April 19, 2022, 1:00 - 4:00 pm (Atlantic time): Analyzing Molecular Dynamics Data with PYTRAJ


  1. Previous experience working with the command line (Linux).
  2. You need to have a laptop with a Mac, Linux or Windows operating system (not a tablet, Chromebook, etc) on which you have administrative privileges, as you will need to pre-load specific software packages.

This session will be delivered online.

Participants must register using their institutional / organizational email address (not a personal email, ie. gmail).

Connections details for the session as well as further preparation information will be sent out prior to the session.

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