- Binding Free Energy Calculations and Molecular Dynamics Studies on Complexes of Viral Proteases with their Ligands - Oliver Anselm Kuhn
Optional OpenMM support when running molecular dynamics simulations using
See the section on free energy calculations under the
- Toward Fast and Accurate Binding Affinity Prediction with
pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration
- OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
- "Derivatives of the potential are not possible in this framework, so thermodynamic integration (TI) cannot be used".
- Alchemical free energy calculations in OpenMM - Describes thermodynamic integration (TI) and Bennett acceptance ratio (BAR) and explains why multistate BAR (MBAR) is better.
- Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs - 200x faster than a single GPU core.
- FESetup - Set up alchemical free energy simulations for Sire, AMBER, GROMACS, or CHARMM.
- alchemical-analysis - Tutorial from the MobleyLab on how to analyze alchemical free energy calculcations conducted in GROMACS, AMBER, or SIRE.
- PyMBAR - Python implementation of the multistate Bennett acceptance ratio (MBAR).
- YANK - See: Add ability to specify protein point mutations,
pmx- Automated Protein Structure and Topology Generation for Alchemical Perturbations. [Paper, Tutorial]
- SOMD Hydration Free Energy Tutorial
- Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan
- Towards computional specificity screening of DNA-binding proteins - Validation of alchemical free energy calculation for interface mutations.
- Calculation of Binding Free Energies - Extensive protocol for alchemical free energy calculations.