MDAnalysis and FHI-aims
MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations. It can handle many classical MD simulation tasks. MDAnalysis also has support for FHI-aims, e.g., reading and writing FHI-aims
geometry.in input files.
In this tutorial, we will show how one can take a frame from a classical force-field based MD trajectory and write it out in FHI-aims format for subsequent use in a FHI-aims run. We also show how one can cut out a partial geometry segment from a larger system and write out this reduced system.
How to use this tutorial
In the left side panel of this site you will find the sections of this tutorial. On the right side you will find a table of contents of the current page.
All files related to this tutorial can be found at https://gitlab.com/FHI-aims-club/tutorials/fhi-aims-mdanalysis/-/tree/master/Tutorial/files .
Assumptions for this tutorial
This tutorial assumes that you are able (or can separately figure out how) to create a molecular dynamics trajectory with another tool. In this example, we will be starting from a trajectory and topology file generated by the GROMACS classical molecular dynamics code.
We also assume that you have a version of FHI-aims installed and running on a compute platform of your choice.
Note that MDAnalysis handles input and output formats from many other codes, so this tutorial is not contingent on being able to produce trajectories specifically using GROMACS. Please see the MDAnalysis website for a full description of the capabilities of MDAnalysis.