4.7 Article

Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations

Journal

JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 19, Issue 6, Pages 1805-1817

Publisher

AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.2c01258

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Performing alchemical transformations is widely used in free energy calculations for biophysical processes. Alchemical methods can fail in certain scenarios, but using alchemical variables in metadynamics can enhance sampling and address these issues. In this study, alchemical metadynamics was validated and shown to accelerate sampling by introducing configurational collective variables. The necessary code changes have been released for general use in PLUMED 2.8.
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 alchemical processes with varying complexities and dimensionalities of collective variable space, including the interconversion between the torsional metastable states of a toy system and the methylation of a nucleoside both in the isolated form and in a duplex. We show that multidimensional alchemical metadynamics can address the challenges mentioned above and further accelerate sampling by introducing configurational collective variables. The method can trivially be combined with other metadynamics-based algorithms implemented in PLUMED. The necessary PLUMED code changes have already been released for general use in PLUMED 2.8.

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