Molecular Dynamics

The dynamic stability of protein conformations has become a key technique in the study of proteins and protein-ligand complexes. Flare™ provides a dedicated interface to create, playback and analyze Molecular Dynamics trajectories.

• Study docking results to determine pose stability through contact frequency analysis
• View initial ligand pose during the trajectory playback to visually assess ligand movements and pose changes
• Easily take snapshots as starting points for further experiments, such as ensemble docking or FEP calculations

Flare enables highly customized or standard configurations for calculations enabling both bespoke and rapid setup of experiments. Key features in dynamics calculations are:

• Multiple force field support – choose AMBER GAFF and GAFF2 or the innovative OpenForceField
• Choose explicit water models with three of four point models for the greatest accuracy
• Run rapid simulations with a choice of many implicit solvent models
• Run longer simulations in a shorter time using Hydrogen Mass Repartitioning and longer time steps
• Ensure the accuracy of your results  by creating custom parameters for your molecules with an accessible force field parameter builder
• Get the most from your hardware with calculations that run on GPUs or CPUs
• Use either local GPUs/CPUs or rely upon the seamless connection to remote calculation resources offered by the Cresset Engine Broker™ to speed up the calculation

The analysis of dynamics trajectories in Flare provides the feedback you need to make decisions.

• Dedicated dynamics dock enables visualization of trajectories in the context of your complete Flare project enabling comparison with starting protein and ligand conformations
• Analyze protein-ligand interactions and custom measurements across all or part of the trajectory
• Gain confidence in your results by analyzing system physical properties like potential energy, temperature, box volume and density
• Flare uses the powerful openMM dynamics engine enabling saving and reading of trajectories in standard DCD format wherever they are calculated