Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

By Yinglong Miao, V. Feher, James Andrew McCammon. Journal of Chemical Theory and Computation, 2015

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A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost potential that follows Gaussian distribution, accurate reweighting of the GaMD simulations is achieved using cumulant expansion to the second order. Here, GaMD is 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.

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/1ff445708caa52b9232b6851cff28c12caf81d8a

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Citations in the corpus

Scalable molecular dynamics on CPU and GPU architectures with NAMD. (2020, methodology): “148 Unlike many other enhanced sampling methods, aMD does not require a predefined reaction-coordinate model.”