Literature DB >> 23901958

Adaptive single replica multiple state transition interface sampling.

Wei-Na Du1, Peter G Bolhuis.   

Abstract

The multiple state transition path sampling method allows sampling of rare transitions between many metastable states, but has the drawback that switching between qualitatively different pathways is difficult. Combination with replica exchange transition interface sampling can in principle alleviate this problem, but requires a large number of simultaneous replicas. Here we remove these drawbacks by introducing a single replica sampling algorithm that samples only one interface at a time, while efficiently walking through the entire path space using a Wang-Landau approach or, alternatively, a fixed bias. We illustrate the method on several model systems: a particle diffusing in a simple 2D potential, isomerization in a small Lennard Jones cluster, and isomerization of the alanine dipeptide in explicit water.

Entities:  

Year:  2013        PMID: 23901958     DOI: 10.1063/1.4813777

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


  7 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.  Beating the millisecond barrier in molecular dynamics simulations.

Authors:  Frank Noé
Journal:  Biophys J       Date:  2015-01-20       Impact factor: 4.033

3.  Equilibrium kinetic network of the villin headpiece in implicit solvent.

Authors:  Weina Du; Peter G Bolhuis
Journal:  Biophys J       Date:  2015-01-20       Impact factor: 4.033

4.  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

Review 5.  Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

Authors:  Tatiana Maximova; Ryan Moffatt; Buyong Ma; Ruth Nussinov; Amarda Shehu
Journal:  PLoS Comput Biol       Date:  2016-04-28       Impact factor: 4.475

Review 6.  Path-sampling strategies for simulating rare events in biomolecular systems.

Authors:  Lillian T Chong; Ali S Saglam; Daniel M Zuckerman
Journal:  Curr Opin Struct Biol       Date:  2016-12-13       Impact factor: 6.809

7.  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

  7 in total

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