Literature DB >> 31438687

Enhanced sampling in molecular dynamics.

Yi Isaac Yang1, Qiang Shao2, Jun Zhang3, Lijiang Yang4, Yi Qin Gao1.   

Abstract

Although molecular dynamics simulations have become a useful tool in essentially all fields of chemistry, condensed matter physics, materials science, and biology, there is still a large gap between the time scale which can be reached in molecular dynamics simulations and that observed in experiments. To address the problem, many enhanced sampling methods were introduced, which effectively extend the time scale being approached in simulations. In this perspective, we review a variety of enhanced sampling methods. We first discuss collective-variables-based methods including metadynamics and variationally enhanced sampling. Then, collective variable free methods such as parallel tempering and integrated tempering methods are presented. At last, we conclude with a brief introduction of some newly developed combinatory methods. We summarize in this perspective not only the theoretical background and numerical implementation of these methods but also the new challenges and prospects in the field of the enhanced sampling.

Year:  2019        PMID: 31438687     DOI: 10.1063/1.5109531

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


  30 in total

1.  Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations.

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2.  Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes.

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Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-12       Impact factor: 11.205

3.  Extrapolation and interpolation strategies for efficiently estimating structural observables as a function of temperature and density.

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Journal:  J Chem Phys       Date:  2020-10-14       Impact factor: 3.488

4.  Machine Learning for Electronically Excited States of Molecules.

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5.  Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders.

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Journal:  J Chem Phys       Date:  2021-11-21       Impact factor: 3.488

Review 6.  Protein Design: From the Aspect of Water Solubility and Stability.

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7.  Enhancing Ligand and Protein Sampling Using Sequential Monte Carlo.

Authors:  Miroslav Suruzhon; Michael S Bodnarchuk; Antonella Ciancetta; Ian D Wall; Jonathan W Essex
Journal:  J Chem Theory Comput       Date:  2022-05-19       Impact factor: 6.578

Review 8.  Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators.

Authors:  Daniel Şterbuleac
Journal:  RSC Med Chem       Date:  2021-07-22

9.  Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning.

Authors:  Gaspar P Pinto; Ondrej Vavra; Sergio M Marques; Jiri Filipovic; David Bednar; Jiri Damborsky
Journal:  Comput Struct Biotechnol J       Date:  2021-05-26       Impact factor: 7.271

Review 10.  Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters.

Authors:  Alioscka A Sousa; Peter Schuck; Sergio A Hassan
Journal:  Nanoscale Adv       Date:  2021-04-28
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