Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables - PubMed

Affiliations

• PMID: 26614317
• DOI: 10.1021/ct9004432

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

Jérome Hénin et al. J Chem Theory Comput. 2010.

Abstract

A new implementation of the adaptive biasing force (ABF) method is described. This implementation supports a wide range of collective variables and can be applied to the computation of multidimensional energy profiles. It is provided to the community as part of a code that implements several analogous methods, including metadynamics. ABF and metadynamics have not previously been tested side by side on identical systems. Here, numerical tests are carried out on processes including conformational changes in model peptides and translocation of a halide ion across a lipid membrane through a peptide nanotube. On the basis of these examples, we discuss similarities and differences between the ABF and metadynamics schemes. Both approaches provide enhanced sampling and free energy profiles in quantitative agreement with each other in different applications. The method of choice depends on the dimension of the reaction coordinate space, the height of the barriers, and the relaxation times of degrees of freedom in the orthogonal space, which are not explicitly described by the chosen collective variables.

Similar articles

• Metadynamics as a tool for exploring free energy landscapes of chemical reactions.

  Ensing B, De Vivo M, Liu Z, Moore P, Klein ML. Ensing B, et al. Acc Chem Res. 2006 Feb;39(2):73-81. doi: 10.1021/ar040198i. Acc Chem Res. 2006. PMID: 16489726

• Taming Rugged Free Energy Landscapes Using an Average Force.

  Fu H, Shao X, Cai W, Chipot C. Fu H, et al. Acc Chem Res. 2019 Nov 19;52(11):3254-3264. doi: 10.1021/acs.accounts.9b00473. Epub 2019 Nov 4. Acc Chem Res. 2019. PMID: 31680510 Review.

• Fast and Accurate Multidimensional Free Energy Integration.

  Hénin J. Hénin J. J Chem Theory Comput. 2021 Nov 9;17(11):6789-6798. doi: 10.1021/acs.jctc.1c00593. Epub 2021 Oct 19. J Chem Theory Comput. 2021. PMID: 34665624

• Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers.

  Jämbeck JP, Lyubartsev AP. Jämbeck JP, et al. J Phys Chem Lett. 2013 Jun 6;4(11):1781-7. doi: 10.1021/jz4007993. Epub 2013 May 14. J Phys Chem Lett. 2013. PMID: 26283109

• Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms.

  Cavalli A, Spitaleri A, Saladino G, Gervasio FL. Cavalli A, et al. Acc Chem Res. 2015 Feb 17;48(2):277-85. doi: 10.1021/ar500356n. Epub 2014 Dec 12. Acc Chem Res. 2015. PMID: 25496113 Review.

Cited by

• Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations.

  Sinko W, de Oliveira CA, Pierce LC, McCammon JA. Sinko W, et al. J Chem Theory Comput. 2012 Jan 10;8(1):17-23. doi: 10.1021/ct200615k. Epub 2011 Nov 21. J Chem Theory Comput. 2012. PMID: 22241967 Free PMC article.

• Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations.

  Sun H, Tian S, Zhou S, Li Y, Li D, Xu L, Shen M, Pan P, Hou T. Sun H, et al. Sci Rep. 2015 Feb 13;5:8457. doi: 10.1038/srep08457. Sci Rep. 2015. PMID: 25678308 Free PMC article.

• Insertion of short amino-functionalized single-walled carbon nanotubes into phospholipid bilayer occurs by passive diffusion.

  Kraszewski S, Bianco A, Tarek M, Ramseyer C. Kraszewski S, et al. PLoS One. 2012;7(7):e40703. doi: 10.1371/journal.pone.0040703. Epub 2012 Jul 16. PLoS One. 2012. PMID: 22815794 Free PMC article.

• A Multi-Scale Approach to Model K⁺ Permeation Through the KcsA Channel.

  Horng TL, Chen RS, Leonardi MV, Franciolini F, Catacuzzeno L. Horng TL, et al. Front Mol Biosci. 2022 Jul 8;9:880660. doi: 10.3389/fmolb.2022.880660. eCollection 2022. Front Mol Biosci. 2022. PMID: 35911957 Free PMC article.

• Tunable Self-Assembly of YF₃ Nanoparticles by Citrate-Mediated Ionic Bridges.

  Martínez-Esaín J, Faraudo J, Puig T, Obradors X, Ros J, Ricart S, Yáñez R. Martínez-Esaín J, et al. J Am Chem Soc. 2018 Feb 14;140(6):2127-2134. doi: 10.1021/jacs.7b09821. Epub 2018 Jan 30. J Am Chem Soc. 2018. PMID: 29308645 Free PMC article.