LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics (MD) code created for simulating molecular and atomic systems such as proteins in solution, liquid-crystals, polymers, zeolites, or simple Lennard-Jonesium.

Chemistry packages for using with the document typesetting system LaTeX. Includes packages for reactions, molecular formulae, R and S codes, chemistry journals, symmetry elements and even to draw chemical structures.

LaueX is an interactive program with a GUI that can simulate a Laue diagram, when given the orientation of the crystal and the cell parameters. LaueX can also index a Laue diagram if the position of experimental spots are provided.

The Lennard-Jones Gas Simulator does a molecular simulation of noble gases.

The Linux for Chemistry project (LfC) is dedicated to compiling the most comprehensive collection of Chemistry software, and making it available for the Linux operating system. LfC provides point-and-click installation, a complete on-line library of searchable documentation, and much more.

The goal of LSD (Logic for Structure Determination) is to help the user propose one or more molecular structures from data that is mainly extracted from 2D NMR spectra.

MacroModel is a molecular modeling software package which allows the user to construct and graphically manipulate both simple and complex chemical structures, to apply molecular mechanics and dynamics techniques to evaluate the energies and geometries of molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations.

Maestro is the unified interface for all Schrodinger software. Impressive rendering capabilities, a powerful selection of analysis tools, and an easy-to-use design combine to make Maestro a versatile modeling environment for all researchers.

MAPS (Materials And Processes Simulations) is a platform for performing materials modeling and simulations. It provides a flexible framework for accessing both proprietary and open-source simulation codes in the areas of quantum, classical, mesoscale and chemical engineering. MAPS serves as an integration tool for all modeling related tasks and data and offers a multi-user/multi-project modeling environment complete with data management.

Marvin is a suite of Java based chemistry software that have different forms: 1. Marvin Applets are made for the Web Developer who builds chemistry-related World Wide Web sites; 2. Marvin Beans are made for the Software Developer who wants to incorporate molecule drawing or visualizing capabilities into his/her application; 3. MarvinSketch is an application for the Chemist or anyone else who wants to draw chemical structures.