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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Installing molSimplify Wednesday, June 10, 2020 Install recommendations: For users who do not intend to develop (i.e., change the source code) with molSimplify, we recommend an install via Docker or Conda, where we maintain a static image of molSimplify that includes machine learning models that we have published. For advanced users who would... (read more) |
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molSimplify Tutorial 13: molscontrol -- an intelligent job control system to manage your DFT geometry optimizations for inorganic discovery. Monday, April 1, 2019 With the static classifier, we achieve great performance on job status predictions of out-of-sample data points, capturing their failure before doing the simulation thus saving lots of computational resources (https://hjkgrp.mit.edu/content/molsimplify-tutorial-12-using-static-clas...). When... (read more) |
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molSimplify Tutorial 12: Using the static classifier to predict your simulation outcomes before they waste your time Monday, March 25, 2019 Geometry optimization with density functional theory (DFT), a general procedure to obtain the ground state structures of a complex, is computationally demanding in terms of time and can also easily fail. Two main failure modes are 1) the expected geometry cannot maintain stability during the DFT... (read more) |
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Using molSimplify in Python scripts Tuesday, February 5, 2019 Many of the classes and methods that are used in molSimplify can be incorporated into your own python scripts. This can be used to extend the geometric manipulation routines in molSimplify to custom use-cases, or to help post-processing the results of DFT calculations. The most useful can be found... (read more) |
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molSimplify Tutorial 11: Transition state structure generation in molSimplify Wednesday, September 5, 2018 Note: TS generation is not currently working as of 10/18/19. Check back here for updates later. Introduction Today we're going to teach you about new features in molSimplify that make it possible to generate transition states in addition to intermediates for inorganic complexes. Currently,... (read more) |
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molSimplify Tutorial 10: Adding ligands to molSimplify Wednesday, May 9, 2018 molSimpliy comes with about 160 built in common ligands and a nifty decoration manager to modify them. However, this cannot hope to address the scope of possible ligands, so we also support providing your own ligands as SMILES or in 3D molecule formats. Let's make a triple bidentate complex with... (read more) |
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QM9 kernel models using molSimplify, RACs and R: Part 1 Tuesday, February 20, 2018 */ In this two-part tutorial, we’ll show you how to use molSimplify to collect autocorrelation-based descriptors from molecular structures and use those to make predictions using a simple kernel ridge regression (KRR) model, as shown in our recent paper. In this first part, we will explain how to... (read more) |
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QM9 kernel models using molSimplify, RACs and R: Part 2 Tuesday, February 20, 2018 */ In the second part of our tutorial, we will demonstrate how to use R to conduct kernel based prediction of atomization energies based on RACs. You’ll need QM9_descriptor_file.csv, which we prepared using molSimplify in the previous tutorial and also provide here. We’ll use R to conduct a simple... (read more) |
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molSimplify Tutorial 9: Bidentate Ligand Replacement Thursday, December 21, 2017 In this tutorial, we will show how to replace multidentate ligands in a prebuilt complex. This feature, which facilitates screening of diverse catalyst scaffolds, was recently added to molSimplify. Today’s example involves the following Zn(II) intermediate in a model carbonic anhydrase catalytic... (read more) |
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molSimplify Tutorial 8: Higher Period Transition Metal Complexes Wednesday, December 6, 2017 So far in our molSimplify tutorials, we have been focusing on generating structures for first row transition metal complexes. While the study of such complexes is certainly crucial for research areas such as catalysis and pharmacology, it is imperative that we also include heavy metal complexes in... (read more) |