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Molecular Dynamics

Wednesday, April 10, 1:30-4:30 p.m.

Online

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 AMBER and NAMD software for preparing 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 two-hour hands-on sessions over two weeks.

Schedule

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

Requirements

  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.

Register here.

For more ACENET events, click here.

Presented by ACENET

Event Listing 2024-04-10 13:30:00 2024-04-10 16:30:00 America/St_Johns Molecular Dynamics 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 AMBER and NAMD software for preparing 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 two-hour hands-on sessions over two weeks. Schedule 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 Requirements Previous experience working with the command line (Linux). 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. Register here. For more ACENET events, click here. Online ACENET