Description
This lesson is an introduction to molecular dynamics (MD) simulations using the LAMMPS package. It will cover the following topics:
- Molecular dynamics simulation fundamentals.
- Creating a LAMMPS input file.
- Using force-fields and creating independant LAMMPS topology (data) files.
- Computing and averaging physical properties during simulation.
- Other software related to LAMMPS input creation, data post-processing, and visualization.
For this lesson, we expect attendees to be familiar with HPC environments. We will not be covering the differences between HPC and regular computing environments. This lesson is aimed at anyone who:
- has experience using
bash(or any other shell). - has an interest in running simulations using LAMMPS.
General Information
Requirements: Participants must have a working laptop or desktop computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have access to a terminal (Max and Linux users should have a terminal installed by default; Windows users should get either MobaXterm or, if they are already familiar with it, Windows Subsystems for Linux (WSL). They are also required to abide by the ARCHER2 Training Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody.
Materials will be provided in advance of the lesson. If we can help making learning easier for you (e.g. sign-language interpreters) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email R.Apostolo@epcc.ed.ac.uk for more information.
Prerequisites
You should have used remote HPC facilities before. In particular, you should be happy with connecting using SSH, know what a batch scheduling system is and be familiar with using the Linux command line. You should also be happy editing plain text files in a remote terminal (or, alternatively, editing them on your local system and copying them to the remote HPC system using
scp).