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]
- 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 Non Equilibrium 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]
- Non-Equilibrium Switching Recovery [Utility] [FECalc]
- Non-Equilibrium 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