Welcome to the TIES MD documentation.

TIES is a collection of software packages to calculate protein ligand binding free energies with physics based alchemical methods. TIES stands for thermodynamic integration with enhanced sampling and can be used to calculate accurate and reproducible relative binding free energies. Please see the theory section for more information on the specifics of this method.

Within the TIES collection there are two packages: TIES 20, TIES MD. TIES 20 is available online and can be used to build all input for TIES MD. TIES MD is an open source implementation of the TIES protocol that is built on OpenMM and NAMD. This document will explain the use of TIES MD software packages please see the TIES 20 website for information on our online system builder.

Contents

• Installation
  • TIES MD
  • TIES OpenMM linux-ppc64le
• Tutorial
  • Getting started
  • Input
  • Command Line
  • Simulation Preparation
  • Running Simulations
  • Analysis
• TIES MD API
  • API
• Binding Free Energy Tutorial
  • General BFE background
  • Setup
  • Running
  • BFE Analysis
• Parallelization
  • TIES-OpenMM
  • TIES-NAMD
• HPC Submission scripts
  • NAMD
  • OpenMM
  • NAMD 3
• Theory
  • Outline
  • Alchemical Calculations
  • Alchemical Pathways
• 🚀Github

Code Documentation

• TIES_MD
  • TIES_MD package