Exploring Valleys without Climbing Every Peak

More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction

James F. Dama, Glen Hocky, Rui Sun, Gregory A. Voth

Research output: Contribution to journalArticle

Abstract

Metadynamics is an enhanced sampling method designed to flatten free energy surfaces uniformly. However, the highest-energy regions are often irrelevant to study and dangerous to explore because systems often change irreversibly in unforeseen ways in response to driving forces in these regions, spoiling the sampling. Introducing an on-the-fly domain restriction allows metadynamics to flatten only up to a specified energy level and no further, improving efficiency and safety while decreasing the pressure on practitioners to design collective variables that are robust to otherwise irrelevant high energy driving. This paper describes a new method that achieves this using sequential on-the-fly estimation of energy wells and redefinition of the metadynamics hill shape, termed metabasin metadynamics. The energy level may be defined a priori or relative to unknown barrier energies estimated on-the-fly. Altering only the hill ensures that the method is compatible with many other advances in metadynamics methodology. The hill shape has a natural interpretation in terms of multiscale dynamics, and the computational overhead in simulation is minimal when studying systems of any reasonable size, for instance proteins or other macromolecules. Three example applications show that the formula is accurate and robust to complex dynamics, making metadynamics significantly more forgiving with respect to CV quality and thus more feasible to apply to the most challenging biomolecular systems.

Original languageEnglish (US)
Pages (from-to)5638-5650
Number of pages13
JournalJournal of Chemical Theory and Computation
Volume11
Issue number12
DOIs
StatePublished - Nov 3 2015

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Electron energy levels
valleys
constrictions
Sampling
Energy barriers
Macromolecules
Free energy
energy levels
sampling
Proteins
energy
macromolecules
safety
free energy
methodology
proteins
simulation

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Cite this

Exploring Valleys without Climbing Every Peak : More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction. / Dama, James F.; Hocky, Glen; Sun, Rui; Voth, Gregory A.

In: Journal of Chemical Theory and Computation, Vol. 11, No. 12, 03.11.2015, p. 5638-5650.

Research output: Contribution to journalArticle

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