Literature DB >> 31575198

Mapping saddles and minima on free energy surfaces using multiple climbing strings.

Gourav Shrivastav1, Eric Vanden-Eijnden2, Cameron F Abrams1.   

Abstract

Locating saddle points on free energy surfaces is key in characterizing multistate transition events in complicated molecular-scale systems. Because these saddle points represent transition states, determining minimum free energy pathways to these saddles and measuring their free energies relative to their connected minima are further necessary, for instance, to estimate transition rates. In this work, we propose a new multistring version of the climbing string method in collective variables to locate all saddles and corresponding pathways on free energy surfaces. The method uses dynamic strings to locate saddles and static strings to keep a history of prior strings converged to saddles. Interaction of the dynamic strings with the static strings is used to avoid the convergence to already-identified saddles. Additionally, because the strings approximate curves in collective-variable space, and we can measure free energy along each curve, identification of any saddle's two connected minima is guaranteed. We demonstrate this method to map the network of stationary points in the 2D and 4D free energy surfaces of alanine dipeptide and alanine tripeptide, respectively.

Entities:  

Year:  2019        PMID: 31575198      PMCID: PMC7043847          DOI: 10.1063/1.5120372

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


  20 in total

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Authors: 
Journal:  Phys Rev Lett       Date:  1996-11-18       Impact factor: 9.161

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Authors:  Baron Peters; Andreas Heyden; Alexis T Bell; Arup Chakraborty
Journal:  J Chem Phys       Date:  2004-05-01       Impact factor: 3.488

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Authors:  Jérôme Hénin; Christophe Chipot
Journal:  J Chem Phys       Date:  2004-08-15       Impact factor: 3.488

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Authors:  Bradley M Dickson; Frédéric Legoll; Tony Lelièvre; Gabriel Stoltz; Paul Fleurat-Lessard
Journal:  J Phys Chem B       Date:  2010-05-06       Impact factor: 2.991

5.  Scalable molecular dynamics with NAMD.

Authors:  James C Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D Skeel; Laxmikant Kalé; Klaus Schulten
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

6.  Finite temperature string method for the study of rare events.

Authors:  Weinan E; Weiqing Ren; Eric Vanden-Eijnden
Journal:  J Phys Chem B       Date:  2005-04-14       Impact factor: 2.991

7.  Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations.

Authors:  Tang-Qing Yu; Mauro Lapelosa; Eric Vanden-Eijnden; Cameron F Abrams
Journal:  J Am Chem Soc       Date:  2015-02-23       Impact factor: 15.419

8.  Efficient and direct generation of multidimensional free energy surfaces via adiabatic dynamics without coordinate transformations.

Authors:  Jerry B Abrams; Mark E Tuckerman
Journal:  J Phys Chem B       Date:  2008-12-11       Impact factor: 2.991

9.  Minimization of polypeptide energy. XI. The method of gentlest ascent.

Authors:  G M Crippen; H A Scheraga
Journal:  Arch Biochem Biophys       Date:  1971-06       Impact factor: 4.013

10.  Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models.

Authors:  Divya Nayar; Charusita Chakravarty
Journal:  J Phys Chem B       Date:  2015-07-16       Impact factor: 2.991

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