Literature DB >> 16851777

Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods?

Harald Oberhofer1, Christoph Dellago, Phillip L Geissler.   

Abstract

We have investigated the maximum computational efficiency of reversible work calculations that change control parameters in a finite amount of time. Because relevant nonequilibrium averages are slow to converge, a bias on the sampling of trajectories can be beneficial. Such a bias, however, can also be employed in conventional methods for computing reversible work, such as thermodynamic integration or umbrella sampling. We present numerical results for a simple one-dimensional model and for a Widom insertion in a soft sphere liquid, indicating that, with an appropriately chosen bias, conventional methods are in fact more efficient. We describe an analogy between nonequilibrium dynamics and mappings between equilibrium ensembles, which suggests that the practical inferiority of fast switching is quite general. Finally, we discuss the relevance of adiabatic invariants in slowly driven Hamiltonian systems for the application of Jarzynski's theorem.

Mesh:

Year:  2005        PMID: 16851777     DOI: 10.1021/jp044556a

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  8 in total

1.  Density-dependent analysis of nonequilibrium paths improves free energy estimates.

Authors:  David D L Minh
Journal:  J Chem Phys       Date:  2009-05-28       Impact factor: 3.488

2.  Protein-protein interaction investigated by steered molecular dynamics: the TCR-pMHC complex.

Authors:  Michel A Cuendet; Olivier Michielin
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

3.  Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages.

Authors:  David D L Minh; John D Chodera
Journal:  J Chem Phys       Date:  2009-10-07       Impact factor: 3.488

4.  Replica exchange with nonequilibrium switches.

Authors:  Andrew J Ballard; Christopher Jarzynski
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-10       Impact factor: 11.205

5.  A generalized linear response framework for expanded ensemble and replica exchange simulations.

Authors:  Brian K Radak; Donghyuk Suh; Benoît Roux
Journal:  J Chem Phys       Date:  2018-08-21       Impact factor: 3.488

Review 6.  Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.

Authors:  Hagai Meirovitch; Srinath Cheluvaraja; Ronald P White
Journal:  Curr Protein Pept Sci       Date:  2009-06       Impact factor: 3.272

Review 7.  Structure-Based, Rational Design of T Cell Receptors.

Authors:  V Zoete; M Irving; M Ferber; M A Cuendet; O Michielin
Journal:  Front Immunol       Date:  2013-09-12       Impact factor: 7.561

Review 8.  Collective variable-based enhanced sampling and machine learning.

Authors:  Ming Chen
Journal:  Eur Phys J B       Date:  2021-10-20       Impact factor: 1.500

  8 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.