Literature DB >> 30354148

Combining Metadynamics and Integrated Tempering Sampling.

Yi Isaac Yang1,2, Haiyang Niu1,2, Michele Parrinello1,2,3.   

Abstract

The simulation of rare events is one of the key problems in atomistic simulations. Toward its solution, a plethora of methods have been proposed. Here we combine two such methods: metadynamics and integrated tempering sampling. In metadynamics, the fluctuations of a carefully chosen collective variable are amplified, while in integrated tempering sampling the system is pushed to visit an approximately uniform interval of energies and allows exploring a range of temperatures in a single run. We describe our approach and apply it to the two prototypical systems a SN2 chemical reaction and to the freezing of silica. The combination of metadynamics and integrated tempering sampling leads to a powerful method. In particular in the case of silica we have measured more than 1 order of magnitude acceleration.

Entities:  

Year:  2018        PMID: 30354148     DOI: 10.1021/acs.jpclett.8b03005

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  4 in total

Review 1.  Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.

Authors:  Xiping Gong; Yumeng Zhang; Jianhan Chen
Journal:  Biomolecules       Date:  2021-09-28

2.  Pathways for the formation of ice polymorphs from water predicted by a metadynamics method.

Authors:  Hiroki Nada
Journal:  Sci Rep       Date:  2020-03-13       Impact factor: 4.379

Review 3.  "Dividing and Conquering" and "Caching" in Molecular Modeling.

Authors:  Xiaoyong Cao; Pu Tian
Journal:  Int J Mol Sci       Date:  2021-05-10       Impact factor: 5.923

Review 4.  Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.

Authors:  Gennady M Verkhivker; Steve Agajanian; Guang Hu; Peng Tao
Journal:  Front Mol Biosci       Date:  2020-07-09
  4 in total

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