Intro to MolSSI’s SEAMM: Install and Quick Calculations

Visualize, Design, and Run Computational Chemistry Calculations for Many Users without Needing to Know the Software

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Created byThe Molecular Sciences Software Institute

Last updated 11/2025

English

What you'll learn

Start thinking about designing computational chemistry calculations from a scientific level instead of a programatic one
Installing and running the SEAMM software
Running basic molecular dynamics simulations
Explore and setup Quantum Chemistry, Classical MD, Semi-Emperical, and other computational chemistry property calculations
Create and run a multi-user capable compute server on their local machine with no pre-requisite expertise

Course content

1 section • 6 lectures • 57m total length

Introduction to the SEAMM and the Course2:37
Installing SEAMM and Everything You DON'T Have to Think About9:31
How to install SEAMM, and where to find documentation. You'll see that SEAMM only really needs to be called to open after being installed, then the command line is not needed to work with it afterwords. So long as you have Conda installed, SEAMM will handle the rest.
Managing SEAMM Add-Ons, Modules, and Available Programs7:32
Learn about the SEAMM add-ons and modules which can be used to develop flowcharts for running scientific calculations. Install what you need, keep up to date in a handy self-contained program which keeps track of all SEAMM-related tools. It also handles creating all the backend services with a simple button press.
Creating Flowcharts for Computational Chemistry in SEAMM10:27
Learn how to create and manipulate flowcharts, the core of defining scientific steps for computing your values. These provide reproducible, citable, and portable descriptions and instructions for your scientific efforts. They take care of all variables, input file configurations, end output flow when passed to the compute services through the dashboard and job server (next lecture).
Running Flowcharts and Multi-User Computation without Needing to Know Servers25:50
Learn about the "compute" side of SEAMM, which is handled through a web-centric dashboard and a back-end job server. Both of these services are created, run, and handled with a single button press from the SEAMM installer (see last lecture). You dont need to know anything about website design, back-end server setup, multiple-compute job handling, or anything else to use these features.

This feature also enables multi-user access to workflows, jobs, inputs, outputs in a fully manageable and administrative way. Gone are the days of twenty Python and shell scripts in an equal number of folders!
This is Just the Start with SEAMM. Let's do More!1:56
This is just the start with SEAMM. In future lessons, we'll cover generating fluid dynamics properties without needing to fuss with individual codes or worry about non-reproducible scripts which may not work on other people's computers.

Requirements

Rudimentary Python
Some molecular chemical theory (upper undergrad or entry grad level),
Have Conda installed
Access to- or running-on a Linux, OSX, or Windows Subsystem for Linux

Description

Learn about the Simulation Environment for Atomistic and Molecular Modeling, or SEAMM, from the Molecular Sciences Software Institute (MolSSI). This software can enable quick and straightforward design and execution of computational molecular science calculations in classical molecular dynamics, quantum chemistry, and semi-empirical methods. No knowledge of the nuances or details of any of these domains is required to run and interpret calculations in any of them.

SEAMM provides a platform to allow multiple users to design, share, cite, and execute complex computations and workflows through a powerful web frontend which can be used just as easily by one person as it can one hundred.

This first course will walk you through how to install SEAMM and manage its two primary interfaces: the Installer and the Flowchart creator. The installer provides a self-contained program to manage all possible SEAMM addons and launch the web server and the back end compute servers from a simple button press. Even running on a local machine for yourself, these processes are generated for you with no web development knowledge needed. The course also walks through a simple calculation for an argon fluid NPT calculation from no starting information to a full simulation with time dependent physical properties and statistical correlation analysis in 4 steps, each of which requires zero knowledge of any of the underlying systems and only high-order understanding of the inputs and outputs.

This is Part 1 of a multi-part lesson series on computational fluid dynamics calculation generation at an atomistic level.

Like this content? Check out our other courses here on Udemy:

Introduction to Quantum Chemistry Simulations
CMake
Cookiecutter for Generating Computational Molecular Sciences Python Codes

Who this course is for:

Chemistry Industrial Professionals looking to perform computational chemistry without knowing all the programs
Graduate students looking to expand their computational chemistry knowledge
Quantum chemists who what to run classical simulations and calculations
Classical simulation chemists who want to run quantum calculations
Research groups who want to coordinate their compute jobs in a central location