Literature DB >> 17677198

Accurate sampling using Langevin dynamics.

Giovanni Bussi1, Michele Parrinello.   

Abstract

We show how to derive a simple integrator for the Langevin equation and illustrate how it is possible to check the accuracy of the obtained distribution on the fly, using the concept of effective energy introduced in a recent paper [J. Chem. Phys. 126, 014101 (2007)]. Our integrator leads to correct sampling also in the difficult high-friction limit. We also show how these ideas can be applied in practical simulations, using a Lennard-Jones crystal as a paradigmatic case.

Year:  2007        PMID: 17677198     DOI: 10.1103/PhysRevE.75.056707

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  29 in total

1.  A coarse-grain three-site-per-nucleotide model for DNA with explicit ions.

Authors:  Gordon S Freeman; Daniel M Hinckley; Juan J de Pablo
Journal:  J Chem Phys       Date:  2011-10-28       Impact factor: 3.488

2.  A Stochastic Algorithm for the Isobaric-Isothermal Ensemble with Ewald Summations for All Long Range Forces.

Authors:  Michele Di Pierro; Ron Elber; Benedict Leimkuhler
Journal:  J Chem Theory Comput       Date:  2015-11-25       Impact factor: 6.006

3.  A mesoscale model of DNA and its renaturation.

Authors:  E J Sambriski; D C Schwartz; J J de Pablo
Journal:  Biophys J       Date:  2009-03-04       Impact factor: 4.033

4.  An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization.

Authors:  Daniel M Hinckley; Gordon S Freeman; Jonathan K Whitmer; Juan J de Pablo
Journal:  J Chem Phys       Date:  2013-10-14       Impact factor: 3.488

5.  3₁₀-helix conformation facilitates the transition of a voltage sensor S4 segment toward the down state.

Authors:  Christine S Schwaiger; Pär Bjelkmar; Berk Hess; Erik Lindahl
Journal:  Biophys J       Date:  2011-03-16       Impact factor: 4.033

6.  Diffusion within the cytoplasm: a mesoscale model of interacting macromolecules.

Authors:  Fabio Trovato; Valentina Tozzini
Journal:  Biophys J       Date:  2014-12-02       Impact factor: 4.033

7.  Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture.

Authors:  Asanga Bandara; Afra Panahi; George A Pantelopulos; Tetsuro Nagai; John E Straub
Journal:  J Chem Phys       Date:  2019-05-28       Impact factor: 3.488

8.  Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions.

Authors:  Tang-Qing Yu; Pei-Yang Chen; Ming Chen; Amit Samanta; Eric Vanden-Eijnden; Mark Tuckerman
Journal:  J Chem Phys       Date:  2014-06-07       Impact factor: 3.488

9.  Kramers turnover: From energy diffusion to spatial diffusion using metadynamics.

Authors:  Pratyush Tiwary; B J Berne
Journal:  J Chem Phys       Date:  2016-04-07       Impact factor: 3.488

10.  Predicting reaction coordinates in energy landscapes with diffusion anisotropy.

Authors:  Pratyush Tiwary; B J Berne
Journal:  J Chem Phys       Date:  2017-10-21       Impact factor: 3.488

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