Simulate Biological Systems with Best-in-Class Tools

Biomolecular processes rely on a variety of dynamic interactions between proteins, ligands, solvents and ions. Often, the specifics of these interactions are difficult to capture via physical experimentation alone due to the short time scales over which they occur. Simulation can help elucidate the energetics of these processes, providing insight into their mechanism of action and properties.

BIOVIA Discovery Studio utilizes best in-class molecular simulation programs, NAMD and CHARMm. Furthermore, Gaussian accelerated Molecular Dynamics (GaMD) is also implemented in the latest release of Discovery Studio for simultaneous unconstrained enhanced sampling and free energy calculations.


  • CHARMm
    • Perform explicit solvent or implicit solvent-based minimizations and Molecular Dynamics (MD) simulations
    • GPU-enabled via DOMDEC and OpenMM
  • NAMD
    • Perform explicit solvent MD simulations
    • Solvate a protein with explicit membrane and run MD simulations
  • DMol3 / CHARMm
    • Calculate single point energies or perform minimizations of receptor-ligand complexes using hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) simulations
  • Implementation of GaMD for simultaneous unconstrained enhanced sampling and free energy calculations
    • Configure and run a GaMD equilibration, automatically parametrizing the boost potentials needed
    • Run and restart GaMD simulations
    • Estimate a free energy landscape from a set of MD trajectories, allowing for statistical reweighting of GaMD simulations

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