Literature DB >> 31703501

Approximating free energy and committor landscapes in standard transition path sampling using virtual interface exchange.

Z Faidon Brotzakis1, Peter G Bolhuis2.   

Abstract

Transition path sampling is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of transition path sampling does not directly provide the free energy landscape nor the kinetics. This drawback has motivated the development of path sampling extensions able to simultaneously access both kinetics and thermodynamics, such as transition interface sampling, and the reweighted path ensemble. However, performing transition interface sampling is more involved than standard two-state transition path sampling and still requires (some) insight into the reaction to define interfaces. While packages that can efficiently compute path ensembles for transition interface sampling are now available, it would be useful to directly compute the free energy from a single standard transition path sampling simulation. To achieve this, we present here an approximate method, denoted virtual interface exchange transition path sampling, that makes use of the rejected pathways in a form of waste recycling. The method yields an approximate reweighted path ensemble that allows an immediate view of the free energy landscape from a standard single transition path sampling simulation, as well as enables a committor analysis.

Year:  2019        PMID: 31703501     DOI: 10.1063/1.5119252

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  2 in total

1.  A method of incorporating rate constants as kinetic constraints in molecular dynamics simulations.

Authors:  Z Faidon Brotzakis; Michele Vendruscolo; Peter G Bolhuis
Journal:  Proc Natl Acad Sci U S A       Date:  2021-01-12       Impact factor: 11.205

2.  Transition Path Sampling Based Calculations of Free Energies for Enzymatic Reactions: The Case of Human Methionine Adenosyl Transferase and Plasmodium vivax Adenosine Deaminase.

Authors:  Sree Ganesh Balasubramani; Steven D Schwartz
Journal:  J Phys Chem B       Date:  2022-07-13       Impact factor: 3.466

  2 in total

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