Tutorials

Thanks to everyone who voted for which topic they’d like to see covered next. It was a close one, but the first subject to hit the minimum threshold was DFT+U. I’d like to encourage you to keep voting - the next topic that has the highest votes next month will be the focus of the September tutorial.

When starting a project, one of the first things we need to do is to build up the system we wish to study. This can be really easy if studying a system with available experimental coordinates or a previous paper.

There are a lot of tools you can use to graph your data. For graphing curves, I think xmgrace is one of the most versatile tools. Today I’ll go over some handy tips and tricks I’ve learned with xmgrace.

When starting any new series of simulations with Quantum-ESPRESSO or any other code, the first thing we need to do is to choose our run parameters. While an experienced computational researcher will have general rules of thumb for what cutoffs or cell sizes to use and how many k-points, it can never hurt to revisit what I’ll call “Convergence 101” to make sure you’re doing things right.

Previously, we looked at how to visualize color-coded trajectories in VMD. Today we’ll look at how we can accomplish a similar effect with PyMOL. First, assuming your trajectory is starting out as an xyz coordinate file, you can convert it to a pdb format with the OpenBabel software package.

The Hubbard U may be straightforwardly calculated from linear response and will vary depending upon the configuration and coordination environment of the transition metal in question. However, results at differing values of U are challenging to compare so most typically we average the calculated values of U for different points along a reaction coordinate.

For molecules and the condensed phase alike, it can be useful to analyze how molecular states are defined by the relative atomic contributions. Visualizing molecular orbitals allows us to identify the overall character of each individual orbital.

This tutorial will focus on how we can determine the vibrational properties of molecules with PWscf and Quantum-ESPRESSO using the phonon code. Before we proceed, you’ll need to make sure you have the ph.

As a continuation of the previous tutorial, I will show you a few more things you can do with VMD along with some tricks for PyMOL. We’ll use a model for the phosphopantetheine tether of acyl carrier proteins.

While XCrysden is a great tool for checking your PWscf input for bugs, visualizing NEB pathways and charge densities, this tutorial will show you how VMD can provide powerful tools for visualizing results as well.