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Can I read Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations on EtoBox?
Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations by Wei-Tse Hsu; Valerio Piomponi; Pascal T. Merz; Giovanni Bussi; Michael R. Shirts is a Physics and Astronomy article available to read on EtoBox.
What is Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations about?
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as protein−ligand binding or the transfer of a molecule between environments. While the sampling of alchemical intermediate states in either parallel (e.g., Hamiltonian replica exchange) or serial manner (e.g., expanded ensemble) can bridge the high-probability regions in the configurational space between two end states of interest, alchemical methods can fail in scenarios where the most important slow degrees of freedom in the configurational space are, in large part, orthogonal to the alchemical variable, or if the system gets trapped in a deep basin extending in both the configurational and alchemical space. To alleviate these issues, we propose to use alchemical variables as an additional dimension in metadynamics, making it possible to both sample collective variables and to enhance sampling in free energy calculations simultaneously. In this study, we validate our implementation of "alchemical metadynamics" in PLUMED with test systems and alchemi
Who reads Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations?
It is typically read by researchers, students, and practitioners in Physics and Astronomy.
- Author
- Wei-Tse Hsu; Valerio Piomponi; Pascal T. Merz; Giovanni Bussi; Michael R. Shirts
- Publisher
- American Chemical Society (ACS)
- Published
- 2023
- Language
- EN
- Field
- Physics and Astronomy (Physical Sciences)