Accelerated MD

In accelerated MD sampling is enhanced by adding a bias potential to the true potential energy of the system.

For examples of previously performed studies in which Accelerated MD was the primary method used, see the following example cases:

• Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket.
• Protein–Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics
• GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling.
• Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand Binding Thermodynamics and Kinetics.
• Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding.
• Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant.
• Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors.
• Ligand Binding Pathways and Conformational Transitions of the HIV Protease.

Accelerated MD was also used in the following examples:

• Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed?