Molecular Dynamics

Tuesday, April 4, 1:30-4:30 p.m.

Online

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 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 4, 2022, 1:00 – 4:00hrs (Atlantic time): Practical considerations for Molecular Dynamics

April 6, 2022, 1:00 – 4:00hrs (Atlantic time): Visualizing Structures with VMD

April 11, 2022, 1:00 – 4:00hrs (Atlantic time): Molecular Dynamics with AMBER and NAMD

April 13, 2022, 1:00 – 4:00hrs (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.

Registration details.

Presented by ACENET

Event Listing 2023-04-04 13:30:00 2023-04-04 16:30:00 America/St_Johns Molecular Dynamics 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 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 4, 2022, 1:00 – 4:00hrs (Atlantic time): Practical considerations for Molecular Dynamics April 6, 2022, 1:00 – 4:00hrs (Atlantic time): Visualizing Structures with VMD April 11, 2022, 1:00 – 4:00hrs (Atlantic time): Molecular Dynamics with AMBER and NAMD April 13, 2022, 1:00 – 4:00hrs (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. Registration details. Online ACENET