Tutorials
This page contains some tutorials that I started while a postdoc at Stanford University. We'd also like to bring you some new tutorials about how to run TeraChem shortly. In the meantime, I'll be posting some elective slides that cover the basics of force fields and electronic structure (density functional theory, wave function theory....). Please let us know what you think (the 'fun' link in the menubar above)!
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molSimplify Tutorial 6: Placing structures on slabs Friday, March 10, 2017 In this follow up to our first link , we are going to describe how to use molSimplify to control the placement of molecules, atoms and complexes on surfaces. We’ll assume you have followed the last tutorial and have a file containing the xyz coordinates of your surface (you might want to relax the... (read more) |
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molSimplify Tutorial 5: Using machine learning to build better structures Monday, February 27, 2017 We have recently implemented an artificial neural network (ANN) in molSimplify – you can read all about it in our recent Chemical Science paper here, but the basic principle is easy to understand. We first collected information from 2700 transition metal complexes that we optimized using DFT, and... (read more) |
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molSimplify Tutorial 3: Custom Core Functionalization Sunday, December 25, 2016 In this tutorial, we'll show how to use molSimplify's custom core functionalization feature. This feature allows new functional groups (FGs) or ligands to be attached to user-specified positions in existing structures, and is most useful for studying the effects of ligand functionalization on... (read more) |
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molSimplify Tutorial 4: Database Searching Sunday, December 25, 2016 In this tutorial, we'll show how to use molSimplify to perform chemical database screening, leveraging on calls to OpenBabel together with useful preprocessing and postprocessing tools for seamless integration with the rest of the molSimplify package. Today, we will demonstrate how to search a... (read more) |
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Guide to Charge Shift Analysis and Fukui Shift Analysis Tuesday, December 13, 2016 Here, we outline the procedure for our recently developed CSA and FSA methods, which provide systematic methods for determining QM region in QM/MM simulation. 1. In charge shift analysis, we introduce the idea that rigidly removing core active site residues and computing the electronic... (read more) |
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molSimplify Tutorial 2: Slab Builder Friday, December 2, 2016 In this tutorial, we are going to introduce the latest molSimplify feature – a tool that allows the construction of periodic geometries and facilitates adsorbing any type of molecule supported by the basic molSimplify onto a slab in various ways. This tool is under development and is only... (read more) |
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New Installation Option for molSimplify Monday, October 31, 2016 We are pleased to announce that molSimplify is now available as a Conda package! Conda is a package and environment manager application that lets users easily download and install python, R, C, Scala, Java and other programs, without needing to worry about dependencies. This means getting... (read more) |
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molSimplify Tutorial 1: Structure Generation Saturday, June 18, 2016 In our first tutorial, we'll briefly discuss how to use molSimplify to generate simple coordination complexes. Our example today is a cobalt porphyrin with an imidazole axial ligand and an empty 6th coordination site. Graphical User Interface Firstly, we'll show how to use the graphical user... (read more) |
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molSimplify: introduction Friday, April 29, 2016 molSimplify is an open source Python code that combines the functionality of OpenBabel with new geometric manipulation routines necessary for the generation of transition metal complexes that are then used as input in electronic structure calculations. The software can generate a variety of... (read more) |
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Fixed atom and boundary condition ab initio molecular dynamics (MD) with TeraChem Monday, February 8, 2016 In this tutorial, we’ll briefly review how to set up fixed atom or boundary condition molecular dynamics calculations in TeraChem. In a fixed atom molecular dynamics calculation, specified atoms are fixed at their initial positions, without physical movements. These calculations are useful for... (read more) |