Long-Time-Scale Predictions from Short-Trajectory Data: A Benchmark Analysis of the Trp-Cage Miniprotein

John Strahan, Adam Antoszewski, Chatipat Lorpaiboon, Bodhi P. Vani, Jonathan Weare, Aaron R. Dinner

Research output: Contribution to journalArticlepeer-review


Elucidating physical mechanisms with statistical confidence from molecular dynamics simulations can be challenging owing to the many degrees of freedom that contribute to collective motions. To address this issue, we recently introduced a dynamical Galerkin approximation (DGA) [ Thiede, E. H. et al. J. Chem. Phys., 150, 2019, 244111 ], in which chemical kinetic statistics that satisfy equations of dynamical operators are represented by a basis expansion. Here, we reformulate this approach, clarifying (and reducing) the dependence on the choice of lag time. We present a new projection of the reactive current onto collective variables and provide improved estimators for rates and committors. We also present simple procedures for constructing suitable smoothly varying basis functions from arbitrary molecular features. To evaluate estimators and basis sets numerically, we generate and carefully validate a data set of short trajectories for the unfolding and folding of the trp-cage miniprotein, a well-studied system. Our analysis demonstrates a comprehensive strategy for characterizing reaction pathways quantitatively.

Original languageEnglish (US)
Pages (from-to)2948-2963
Number of pages16
JournalJournal of chemical theory and computation
Issue number5
StatePublished - May 11 2021


  • Molecular Dynamics Simulation
  • Protein Folding
  • Proteins/chemistry

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry


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