Literature DB >> 21054008

The reweighted path ensemble.

Jutta Rogal1, Wolfgang Lechner, Jarek Juraszek, Bernd Ensing, Peter G Bolhuis.   

Abstract

We introduce a reweighting scheme for the path ensembles in the transition interface sampling framework. The reweighting allows for the analysis of free energy landscapes and committor projections in any collective variable space. We illustrate the reweighting scheme on a two dimensional potential with a nonlinear reaction coordinate and on a more realistic simulation of the Trp-cage folding process. We suggest that the reweighted path ensemble can be used to optimize possible nonlinear reaction coordinates.

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Year:  2010        PMID： 21054008     DOI： 10.1063/1.3491817

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


  9 in total

1.  Rotational diffusion affects the dynamical self-assembly pathways of patchy particles.

Authors:  Arthur C Newton; Jan Groenewold; Willem K Kegel; Peter G Bolhuis
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-30       Impact factor: 11.205

2.  A method of incorporating rate constants as kinetic constraints in molecular dynamics simulations.

Authors:  Z Faidon Brotzakis; Michele Vendruscolo; Peter G Bolhuis
Journal:  Proc Natl Acad Sci U S A       Date:  2021-01-12       Impact factor: 11.205

3.  The role of multivalency in the association kinetics of patchy particle complexes.

Authors:  Arthur C Newton; Jan Groenewold; Willem K Kegel; Peter G Bolhuis
Journal:  J Chem Phys       Date:  2017-06-21       Impact factor: 3.488

4.  Simulating rare events using a weighted ensemble-based string method.

Authors:  Joshua L Adelman; Michael Grabe
Journal:  J Chem Phys       Date:  2013-01-28       Impact factor: 3.488

5.  Local initiation conditions for water autoionization.

Authors:  Mahmoud Moqadam; Anders Lervik; Enrico Riccardi; Vishwesh Venkatraman; Bjørn Kåre Alsberg; Titus S van Erp
Journal:  Proc Natl Acad Sci U S A       Date:  2018-04-30       Impact factor: 11.205

6.  Toward Identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method.

Authors:  Dimitri Antoniou; Steven D Schwartz
Journal:  J Phys Chem B       Date:  2011-02-21       Impact factor: 2.991

7.  Transition Path Sampling Based Calculations of Free Energies for Enzymatic Reactions: The Case of Human Methionine Adenosyl Transferase and Plasmodium vivax Adenosine Deaminase.

Authors:  Sree Ganesh Balasubramani; Steven D Schwartz
Journal:  J Phys Chem B       Date:  2022-07-13       Impact factor: 3.466

8.  OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics.

Authors:  David W H Swenson; Jan-Hendrik Prinz; Frank Noe; John D Chodera; Peter G Bolhuis
Journal:  J Chem Theory Comput       Date:  2018-12-31       Impact factor: 6.006

9.  Rate Prediction for Homogeneous Nucleation of Methane Hydrate at Moderate Supersaturation Using Transition Interface Sampling.

Authors:  A Arjun; P G Bolhuis
Journal:  J Phys Chem B       Date:  2020-09-08       Impact factor: 2.991
  9 in total

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