Introduction¶
This package is for running MD simulations useful for drug discovery.

New Protocol of the MD Stage in Lead Optimization¶
In the classic structure-based lead optimization (left in Figure New Protocol of the MD Stage in Lead Optimization), we’ve proposed the two MD stages at the bottom of the funnel: the light and fast MD screening stage, and the computationally more intense free energy calculation stage.
The Floes in the package for each MD stage are:
Light, fast MD screening
Short Trajectory MD with Analysis Floe with 2 ns of the bound state production time
Relative binding free energy (RBFE)
Ligand Bound and Unbound Equilibration for NES Floe
Edge Mapper for RBFE calculations Floe
Non-Equilibrium Switching Floe
You can use Equilibration and Non Equilibrium Switching Floe, which is the combined Floe of Ligand Bound and Unbound Equilibration for NES and Non-Equilibrium Switching Floes.
Or, you can simply combine the two MD stages and run
Short Trajectory MD with Analysis Floe with 6 ns of the bound state production time
Edge Mapper for RBFE calculations Floe
Non-Equilibrium Switching Floe
To get the information on the other Floes in the package, please refer to MDOrion Floes - Documentation in the left panel.