Hyperdynamics - Gaussian Accelerated Molecular Dynamics

Gaussian Accelerated Molecular Dynamics (GaMD) is a biomolecular enhanced sampling method that works by adding a harmonic boost potential to smoothen the system potential energy surface. By constructing a boost potential that follows Gaussian distribution, accurate reweighting of the GaMD simulations is achieved using cumulant expansion to the second order. GaMD has been demonstrated on three biomolecular model systems: alanine dipeptide, chignolin folding and ligand binding to the T4-lysozyme. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of these biomolecules. Furthermore, the free energy profiles obtained from reweighting of the GaMD simulations allow us to identify distinct low energy states of the biomolecules and characterize the protein folding and ligand binding pathways quantitatively.

GaMD scheme

Reference:

Miao, Y.; Feher, V. A.; McCammon, J. A., Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J. Chem. Theory Comput. 2015, 11, 3584-3595.


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Last updated: Tue, November 22, 2016