Welcome to Small Molecule Conformer Generation’s documentation!

SM_ConfGen is a Python package providing a method of generating ligand conformers from Temperature Replic Exchange Molecular Dynamics (TREMD) simulations in GROMACS.

Getting started:

• 1. Getting Started
• 2. Installation
  • 2.1. Requirements
  • 2.2. Installation from source

Theory:

• 1. Basic idea
• 2. Selecting Temperature Windows
• 2. Analyzing Conformers

Launching SM_ConfGen simulations:

• 1. Command-line interface (CLI)
  • 1.1. CLI prep_ConfGen
  • 1.2. CLI run_ConfGen
  • 1.3. CLI analyze_ConfGen
• 2. Input YAML parameters

Indices and tables

• Index