5,450
Views
57
CrossRef citations to date
0
Altmetric
Articles

A review of advancements in coarse-grained molecular dynamics simulations

&
Pages 786-803 | Received 05 May 2020, Accepted 21 Sep 2020, Published online: 11 Oct 2020

Keep up to date with the latest research on this topic with citation updates for this article.

Read on this site (3)

Yan Li, Ye Liu, Boya Yang, Guohui Li & Huiying Chu. (2023) Polarizable atomic multipole-based force field for cholesterol. Journal of Biomolecular Structure and Dynamics 0:0, pages 1-11.
Read now
Tianze Zheng, Yao Zhang, Jiaxin Shi, Jun Xu & Baohua Guo. (2021) Revealing the role of hydrogen bonding in polyurea with multiscale simulations. Molecular Simulation 47:15, pages 1258-1272.
Read now

Articles from other publishers (54)

Cheng Xing, P. Chen & Lei Zhang. (2023) Computational insight into stability-enhanced systems of anthocyanin with protein/peptide. Food Chemistry: Molecular Sciences 6, pages 100168.
Crossref
Katarzyna Malec, Serena Monaco, Ignacio Delso, Justyna Nestorowicz, Marta Kozakiewicz-Latała, Bożena Karolewicz, Yaroslav Z. Khimyak, Jesús Angulo & Karol P. Nartowski. (2023) Unravelling the mechanisms of drugs partitioning phenomena in micellar systems via NMR spectroscopy. Journal of Colloid and Interface Science 638, pages 135-148.
Crossref
Andreas Krämer, Aleksander E. P. Durumeric, Nicholas E. Charron, Yaoyi Chen, Cecilia Clementi & Frank Noé. (2023) Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. The Journal of Physical Chemistry Letters, pages 3970-3979.
Crossref
Andrew J. Lew & Markus J. Buehler. (2023) Single-shot forward and inverse hierarchical architected materials design for nonlinear mechanical properties using an Attention-Diffusion model. Materials Today.
Crossref
Eleonora Ricci & Niki Vergadou. (2023) Integrating Machine Learning in the Coarse-Grained Molecular Simulation of Polymers. The Journal of Physical Chemistry B 127:11, pages 2302-2322.
Crossref
Azadeh Kordzadeh, Mahdi Zarif & Sepideh Amjad-Iranagh. (2023) Molecular dynamics insight of interaction between the functionalized-carbon nanotube and cancerous cell membrane in doxorubicin delivery. Computer Methods and Programs in Biomedicine 230, pages 107332.
Crossref
Frank Hirschmann, Hender Lopez, Felix Roosen-Runge, Tilo Seydel, Frank Schreiber & Martin Oettel. (2023) Effects of flexibility in coarse-grained models for bovine serum albumin and immunoglobulin G. The Journal of Chemical Physics 158:8, pages 084112.
Crossref
Sven Johann Bohr, Fei Wang, Michael Metze, Josipa Lisičar Vukušić, Andreas Sapalidis, Mathias Ulbricht, Britta Nestler & Stéphan Barbe. (2023) State-of-the-art review of porous polymer membrane formation characterization—How numerical and experimental approaches dovetail to drive innovation. Frontiers in Sustainability 4.
Crossref
Abhishek T. Sose, Soumil Y. Joshi, Lakshmi Kumar Kunche, Fangxi Wang & Sanket A. Deshmukh. (2023) A review of recent advances and applications of machine learning in tribology. Physical Chemistry Chemical Physics 25:6, pages 4408-4443.
Crossref
Marcelo C.R. Melo & Rafael C. Bernardi. (2023) Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike. Biophysical Journal.
Crossref
Sajjad Heydari, Stefano Raniolo, Lorenzo Livi & Vittorio Limongelli. (2023) Transferring chemical and energetic knowledge between molecular systems with machine learning. Communications Chemistry 6:1.
Crossref
Jieqiong Zhang, Fei Han, Zihao Yang & Junzhi Cui. (2023) Coupling of an atomistic model and bond-based peridynamic model using an extended Arlequin framework. Computer Methods in Applied Mechanics and Engineering 403, pages 115663.
Crossref
Siewert J. Marrink, Luca Monticelli, Manuel N. Melo, Riccardo Alessandri, D. Peter Tieleman & Paulo C. T. Souza. (2022) Two decades of Martini: Better beads, broader scope. WIREs Computational Molecular Science 13:1.
Crossref
Li Shao, Jinrong Ma, Jesse L. Prelesnik, Yicheng Zhou, Mary Nguyen, Mingfei Zhao, Samson A. Jenekhe, Sergei V. Kalinin, Andrew L. Ferguson, Jim Pfaendtner, Christopher J. Mundy, James J. De Yoreo, François Baneyx & Chun-Long Chen. (2022) Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction. Chemical Reviews 122:24, pages 17397-17478.
Crossref
Saientan Bag, Melissa K. Meinel & Florian Müller-Plathe. (2022) Toward a Mobility-Preserving Coarse-Grained Model: A Data-Driven Approach. Journal of Chemical Theory and Computation 18:12, pages 7108-7120.
Crossref
Yuhua Huang, Yuqi Zhou, Jinming Li & Fulong Zhu. (2022) Materials removal mechanism and multi modes feature for silicon carbide during scratching. International Journal of Mechanical Sciences 235, pages 107719.
Crossref
Manpreet Bagga, Charlotte Hamley-Bennett, Aleena Alex, Brubeck L Freeman, Ismael Justo-Reinoso, Iulia C Mihai, Susanne Gebhard, Kevin Paine, Anthony D Jefferson, Enrico Masoero & Irina D Ofiţeru. (2022) Advancements in bacteria based self-healing concrete and the promise of modelling. Construction and Building Materials 358, pages 129412.
Crossref
Marta Bordonhos, Tiago L. P. Galvão, José R. B. Gomes, José D. Gouveia, Miguel Jorge, Mirtha A. O. Lourenço, José M. Pereira, Germán Pérez‐Sánchez, Moisés L. Pinto, Carlos M. Silva, João Tedim & Bruno Zêzere. (2022) Multiscale Computational Approaches toward the Understanding of Materials. Advanced Theory and Simulations.
Crossref
Philipp Nicolas Depta, Maksym Dosta, Wolfgang Wenzel, Mariana Kozlowska & Stefan Heinrich. (2022) Hierarchical Coarse-Grained Strategy for Macromolecular Self-Assembly: Application to Hepatitis B Virus-Like Particles. International Journal of Molecular Sciences 23:23, pages 14699.
Crossref
Zakiya Shireen, Hansani Weeratunge, Adrian Menzel, Andrew W. Phillips, Ronald G. Larson, Kate Smith-Miles & Elnaz Hajizadeh. (2022) A machine learning enabled hybrid optimization framework for efficient coarse-graining of a model polymer. npj Computational Materials 8:1.
Crossref
Jaehyeok Jin, Alexander J. Pak, Aleksander E. P. Durumeric, Timothy D. Loose & Gregory A. Voth. (2022) Bottom-up Coarse-Graining: Principles and Perspectives. Journal of Chemical Theory and Computation 18:10, pages 5759-5791.
Crossref
Margarita Colberg & Jeremy Schofield. (2022) Configurational entropy, transition rates, and optimal interactions for rapid folding in coarse-grained model proteins. The Journal of Chemical Physics 157:12.
Crossref
Emerson P. Lyra & Luís F. M. Franco. (2022) Deriving force fields with a multiscale approach: From ab initio calculations to molecular-based equations of state . The Journal of Chemical Physics 157:11, pages 114107.
Crossref
Chris Avery, John Patterson, Tyler Grear, Theodore Frater & Donald J. Jacobs. (2022) Protein Function Analysis through Machine Learning. Biomolecules 12:9, pages 1246.
Crossref
Morgan M. Cencer, Benjamin A. Suslick & Jeffrey S. Moore. (2022) From skeptic to believer: The power of models. Tetrahedron 123, pages 132984.
Crossref
Sousa Javan Nikkhah & Matthias Vandichel. (2022) Modeling Polyzwitterion-Based Drug Delivery Platforms: A Perspective of the Current State-of-the-Art and Beyond. ACS Engineering Au 2:4, pages 274-294.
Crossref
Valery Lutsyk, Pawel Wolski & Wojciech Plazinski. (2022) Extending the Martini 3 Coarse-Grained Force Field to Carbohydrates. Journal of Chemical Theory and Computation 18:8, pages 5089-5107.
Crossref
Shuvam Mukherjee, Subrata Jana, Sadhana Khawas, Jintawee Kicuntod, Manfred Marschall, Bimalendu Ray & Sayani Ray. (2022) Synthesis, molecular features and biological activities of modified plant polysaccharides. Carbohydrate Polymers 289, pages 119299.
Crossref
Huimin Gao, Rui Shi, Youliang Zhu, Hujun Qian & Zhongyuan Lu. (2022) Coarse-grained Dynamics Simulation in Polymer Systems: from Structures to Material Properties. Chemical Research in Chinese Universities 38:3, pages 653-670.
Crossref
Tianzhuo Gong & Chunli Han. (2022) Construction of an Intelligent Arrangement Model for Vocal Music Based on HPC Cluster Programming. Scientific Programming 2022, pages 1-13.
Crossref
Dwi Hudiyanti, Sherllyn Meida Christa, Nur Hanna Mardhiyyah, Daru Seto Bagus Anugrah, Tatik Widiarih & Parsaoran Siahaan. (2022) Dynamics insights into aggregation of phospholipid species with cholesterol and vitamin C. Pharmacia 69:2, pages 385-391.
Crossref
Vladimir P. Zhdanov. (2022) Lipid nanoparticles with ionizable lipids: Statistical aspects. Physical Review E 105:4.
Crossref
Petch Khunpetch, Arghya Majee & Rudolf Podgornik. (2022) Curvature effects in charge-regulated lipid bilayers. Soft Matter 18:13, pages 2597-2610.
Crossref
Raphaël Robidas & Claude Y. Legault. (2022) CalcUS: An Open-Source Quantum Chemistry Web Platform. Journal of Chemical Information and Modeling 62:5, pages 1147-1153.
Crossref
Tyler D. Stoffel, Justin B. Haskins, John W. Lawson & Sergiy Markutsya. (2022) Coarse-Grained Dynamically Accurate Simulations of Ionic Liquids: [pyr14][TFSI] and [EMIM][BF 4 ] . The Journal of Physical Chemistry B 126:8, pages 1819-1829.
Crossref
L. Dai, S. Chakraborty, G. Wu, J. Ye, Y. H. Lau, H. Ramanarayan & D. T. Wu. (2022) Molecular simulation of linear octacosane via a CG10 coarse grain scheme . Physical Chemistry Chemical Physics 24:9, pages 5351-5359.
Crossref
Jonathan Utterson & Radek Erban. (2022) On standardised moments of force distribution in simple liquids. Physical Chemistry Chemical Physics 24:9, pages 5646-5657.
Crossref
Tarak K. Patra. (2021) Data-Driven Methods for Accelerating Polymer Design. ACS Polymers Au 2:1, pages 8-26.
Crossref
Abhishek T. Sose, Esmat Mohammadi, Preeya F. Achari & Sanket A. Deshmukh. (2022) Determination of Accurate Interaction Parameters between the Molybdenum Disulfide and Water to Investigate Their Interfacial Properties. The Journal of Physical Chemistry C 126:4, pages 2013-2022.
Crossref
Danh Nguyen, Lei Tao & Ying Li. (2022) Integration of Machine Learning and Coarse-Grained Molecular Simulations for Polymer Materials: Physical Understandings and Molecular Design. Frontiers in Chemistry 9.
Crossref
Dmitry Tolmachev, Natalia Lukasheva, Ruslan Ramazanov, Victor Nazarychev, Natalia Borzdun, Igor Volgin, Maria Andreeva, Artyom Glova, Sofia Melnikova, Alexey Dobrovskiy, Steven A. Silber, Sergey Larin, Rafael Maglia de Souza, Mauro Carlos Costa Ribeiro, Sergey Lyulin & Mikko Karttunen. (2022) Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives. International Journal of Molecular Sciences 23:2, pages 645.
Crossref
Petteri Vainikka, Sebastian Thallmair, Paulo Cesar Telles Souza & Siewert J. Marrink. (2021) Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents: Thermodynamic, Structural, and Extraction Properties. ACS Sustainable Chemistry & Engineering 9:51, pages 17338-17350.
Crossref
Satyen Dhamankar & Michael A. Webb. (2021) Chemically specific coarse‐graining of polymers: Methods and prospects. Journal of Polymer Science 59:22, pages 2613-2643.
Crossref
Thomas C. NicholasEugeny V. Alexandrov, Vladislav A. Blatov, Alexander P. Shevchenko, Davide M. Proserpio, Andrew L. GoodwinVolker L. Deringer. (2021) Visualization and Quantification of Geometric Diversity in Metal–Organic Frameworks. Chemistry of Materials 33:21, pages 8289-8300.
Crossref
Francesco Maria Bellussi, Otello Maria Roscioni, Matteo RicciMatteo Fasano. (2021) Anisotropic Electrostatic Interactions in Coarse-Grained Water Models to Enhance the Accuracy and Speed-Up Factor of Mesoscopic Simulations. The Journal of Physical Chemistry B 125:43, pages 12020-12027.
Crossref
Tomasz Róg, Mykhailo Girych & Alex Bunker. (2021) Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals 14:10, pages 1062.
Crossref
Reza Maleki, Sima Rezvantalab & Mohammad-Ali Shahbazi. (2021) Role of molecular simulation in the future of nanomedicine. Nanomedicine 16:24, pages 2133-2136.
Crossref
Paul Zaby, Johannes Ingenmey, Barbara Kirchner, Stefan Grimme & Sebastian Ehlert. (2021) Calculation of improved enthalpy and entropy of vaporization by a modified partition function in quantum cluster equilibrium theory. The Journal of Chemical Physics 155:10.
Crossref
Alžbeta Kubincová, Sereina Riniker & Philippe H. Hünenberger. (2021) Solvent-scaling as an alternative to coarse-graining in adaptive-resolution simulations: The adaptive solvent-scaling (AdSoS) scheme. The Journal of Chemical Physics 155:9.
Crossref
Evan Pretti & M. Scott Shell. (2021) A microcanonical approach to temperature-transferable coarse-grained models using the relative entropy. The Journal of Chemical Physics 155:9.
Crossref
Chaofu Wu, Kewen Li, Xutao Ning & Lei Zhang. (2021) An Enhanced Scheme for Multiscale Modeling of Thermomechanical Properties of Polymer Bulks. The Journal of Physical Chemistry B 125:30, pages 8612-8626.
Crossref
Siwei Luo & Mark Thachuk. (2021) Conservative Potentials for a Lattice-Mapped Coarse-Grained Scheme. The Journal of Physical Chemistry A 125:29, pages 6486-6497.
Crossref
Xiaoyong Cao & Pu Tian. (2021) “Dividing and Conquering” and “Caching” in Molecular Modeling. International Journal of Molecular Sciences 22:9, pages 5053.
Crossref
Alessandro Marchetto, Zeineb Si Chaib, Carlo Alberto Rossi, Rui Ribeiro, Sergio Pantano, Giulia Rossetti & Alejandro Giorgetti. (2020) CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations. Molecules 25:24, pages 5934.
Crossref

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.