Setting up and Running Molecular Dynamics Simulations: Good Practice and Pitfalls

Aimed at:

Anyone interested learning how to set up and run molecular dynamics simulations.

Requirements:

Basic knowledge of the Linux command line.

Abstract:

Whether you are a user of Amber, Charmm, Gromacs, NAMD or any other MD package, there are a good number of on-line tutorials that will take you through the mechanics of setting up and running an MD simulation. However in general there is less discussion in these about how to ensure you end up with a good simulation. In this workshop we will explore some of the issues in simulation preparation and execution that can trip up the unwary, and how to avoid them.

Training Material

The workshop consists of a series of Jupyter notebooks. These are available below, and can be run using the workshop jupyter server.

Once you have started the server, navigate to the md_workshop directory and you will find the notebooks there.

Contents

Basic_Analaysis/Basic analysis.ipynb (answers)

Something

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