Theory

See a PDF copy included in the GaMD-Amber manual: GaMD_Amber-manual.pdf

1. Gaussian accelerated molecular dynamics (GaMD)

Gaussian accelerated molecular dynamics (GaMD) enhances the conformational sampling of biomolecules by adding a harmonic boost potential to smoothen the system potential energy surface:

GaMD scheme

GaMD Theory

2. Energetic Reweighting using Cumulant Expansion to the Second Order (Gaussian Approximation)

GaMD Energetic Reweighting

3. Ligand Gaussian accelerated molecular dynamics (LiGaMD)

LiGaMD Theory

4. Kinetic reweighting of GaMD simulations with Kramers’ Rate Theory

GaMD Kinetic Reweighting
GaMD Kinetic Reweighting


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◇ Last updated: Mon, July 18, 2022