Molecular Dynamics Affinity Package Documentation¶
The Molecular Dynamics Affinity package provides capability to run certain kinds of MD simulations in Orion.
- Introduction
- How-To Guide and Tutorials
- MD Affinity Floes - Documentation
- Analyze Protein-Ligand MD [MDAnalysis]
- Associate Force Field Offxml Files With Ligand Record [Utility]
- Bound Protein-Ligand MD [MDPrep] [MDRun]
- Compare Experimental Affinity with End Point Analysis Results [Utility]
- Compare Induced-Fit Posing (IFP) Results to Target Receptor [IFP]
- Convert MD Analysis results to Cluster-Centric Dataset [Utility]
- Edge Mapper for RBFE calculations [FECalc]
- Equilibration and Nonequilibrium Switching [MDPrep] [MDRun] [FECalc]
- Extract Short Trajectory MD Results for Download [Utility]
- Induced-Fit Posing (Confined) [IFP]
- Induced-Fit Posing (IFP) Prep: Pruning reference receptor for docking [IFP]
- Ligand Bound and Unbound Equilibration for NES [MDPrep] [MDRun]
- MD API Dataset Converter [Utility]
- NES Result Utilities [Utility] [FECalc]
- Nonequilibrium Switching Recovery [Utility] [FECalc]
- Nonequilibrium Switching [MDRun] [FECalc]
- Plain Gromacs [MDRun]
- Plain Molecular Dynamics [MDRun]
- Short Trajectory MD with Analysis [MDPrep] [MDRun] [MDAnalysis] [STMD]
- Solvate and Run MD [MDPrep] [MDRun]
- oemdaffinity.cubes - Cube Documentation
- Release Notes
- v 6.3.6 April 2024
- v 6.2.1 February 2024
- v 6.1.7 September 2023
- v 6.1.4 September 2023
- v 6.1.2 July 2023
- v 6.0.3 April 2023
- v 5.6.1 December 2022
- v 5.5.3 September 2022
- v 5.5.0 July 2022
- v 5.0.5 April 2022
- v 5.0.3 December 2021
- v 4.0.1 June 2021
- v3.0.1 November 2020
- v2.0.0 September 2020
- v1.0.0
- v0.9.6
- v0.9.4