Gaussian accelerated molecular dynamics (GaMD) is a robust computational technique that provides simultaneous unconstrained enhanced sampling and free energy calculations of large biomolecules. GaMD works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce the energy barriers. Compared with conventional molecular dynamics, GaMD accelerates biomolecular simulations by orders of magnitude. Without the need to set predefined collective variables, GaMD is advantageous for studying complex biological processes with no constraints applied in the simulations. Furthermore, because the boost potential follows a Gaussian distribution, the original free energy profiles of biomolecules can be recovered through cumulant expansion to the second order (“Gaussian approximation”). GaMD allows us to more accurately characterize biomolecular dynamics. Here, new developments of the GaMD method and our recent applications of GaMD in particularly enhanced sampling of ligand binding and protein-protein interactions will be presented.

Gaussian accelerated molecular dynamics (GaMD): Enhanced sampling of ligand binding and protein-protein interactions

2019 Spring National Meeting

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