Introduction

This package is for running MD simulations useful for drug discovery, with floes geared towards MD experts (General MD) and floes also suitable for MD non-experts (Specialized MD). Aside from the most general floes, the underlying design of the floes is towards simulating complexes between a protein and a set of small-molecule ligands in explicit water, with periodic boundary conditions. The solutes are assumed to be prepared and ready for such physics-based modeling.

Specialized MD

These floes carry out more focused MD tasks frequently needed in drug discovery, particularly in lead optimization. Suitable for either MD experts or non-experts, the protein and ligand inputs do require preparation appropriate for physics-based modeling but less stringent than for General MD. These floes perform typical analyses of the results suitable for quick, actionable interpretation by non-experts in addition to access to the MD trajectory for more specialized interpretation by experts.

General MD

These floes have the usual stringent requirements for the preparation for input datasets and produce simply the MD trajectory and standard output from the MD engine. This places a relatively high onus on the user to prepare MD-ready input and to access and analyze the results using their own procedures.