Omnia is a suite of tools for molecular simulation. It covers the entire workflow from model building through simulation to data analysis.
A core principle of the Omnia suite is that all the tools provide compatible Python APIs. By writing Python scripts, you can combine them in powerful ways to define your own workflows for simulation and analysis. This makes Omnia into far more than a set of discrete tools. It is a true integrated workbench for molecular simulation.
- OpenMM. This is the molecular dynamics engine at the core of Omnia. It provides very high performance on both GPUs and CPUs, along with extreme flexibility to support a huge range of simulation protocols.
- MDTraj. This is a library for analysis of molecular dynamics trajectories. It provides many common computations, such as RMSD, secondary structure identification, hydrogen bond identification, etc. It also can read and write many different trajectory file formats.
- PDBFixer. This is a tool for cleaning up molecular structures in preparation for simulating them. It can add missing atoms, replace nonstandard residues by standard ones, build a water box, and more.
- MSMBuilder. This automates the construction and analysis of Markov State Models. It allows you to explore the entire conformational landscape of a system and study dynamics within that landscape.
- Yank. This is a tool for running alchemical free energy calculations. It can efficiently determine ligand binding affinities in both implicit and explicit solvent.