Living journal of computational molecular science最新文献_第3页

Simulation Best Practices for Lipid Membranes [Article v1.0]. 脂质膜模拟最佳实践[文章 v1.0]。

Living journal of computational molecular science Pub Date : 2019-01-09 DOI: 10.33011/livecoms.1.1.5966

David J Smith, Jeffery B Klauda, Alexander J Sodt

{"title":"Simulation Best Practices for Lipid Membranes [Article v1.0].","authors":"David J Smith, Jeffery B Klauda, Alexander J Sodt","doi":"10.33011/livecoms.1.1.5966","DOIUrl":"10.33011/livecoms.1.1.5966","url":null,"abstract":"We establish a reliable and robust standardization of settings for practical molecular dynamics (MD) simulations of pure and mixed (single- and multi-component) lipid bilayer membranes. In lipid membranes research, particle-based molecular simulations are a powerful tool alongside continuum theory, lipidomics, and model, in vitro, and in vivo experiments. Molecular simulations can provide precise and reproducible spatiotemporal (atomic- and femtosecond-level) information about membrane structure, mechanics, thermodynamics, kinetics, and dynamics. Yet the simulation of lipid membranes can be a daunting task, given the uniqueness of lipid membranes relative to conventional liquid-liquid and solid-liquid interfaces, the immense and complex thermodynamic and statistical mechanical theory, the diversity of multiscale lipid models, limitations of modern computing power, the difficulty and ambiguity of simulation controls, finite size effects, competitive continuum simulation alternatives, and the desired application, including vesicle experiments and biological membranes. These issues can complicate an essential understanding of the field of lipid membranes, and create major bottlenecks to simulation advancement. In this article, we clarify these issues and present a consistent, thorough, and user-friendly framework for the design of state-of-the-art lipid membrane MD simulations. We hope to allow early-career researchers to quickly overcome common obstacles in the field of lipid membranes and reach maximal impact in their simulations.","PeriodicalId":74084,"journal":{"name":"Living journal of computational molecular science","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9534443/pdf/nihms-1799309.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33490782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Best Practices for Foundations in Molecular Simulations [Article v1.0]. 分子模拟基础的最佳实践[文章v1.0]。

Living journal of computational molecular science Pub Date : 2019-01-01 Epub Date: 2018-11-29 DOI: 10.33011/livecoms.1.1.5957

Efrem Braun, Justin Gilmer, Heather B Mayes, David L Mobley, Jacob I Monroe, Samarjeet Prasad, Daniel M Zuckerman

引用次数: 114

From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0] 从蛋白质到扰动哈密顿量:GROMACS-2018分子模拟包的一套教程[文章v1.0]

Living journal of computational molecular science Pub Date : 2019-01-01 DOI: 10.33011/LIVECOMS.1.1.5068

Justin A. Lemkul

{"title":"From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0]","authors":"Justin A. Lemkul","doi":"10.33011/LIVECOMS.1.1.5068","DOIUrl":"https://doi.org/10.33011/LIVECOMS.1.1.5068","url":null,"abstract":"This LiveCoMS document is maintained online on GitHub at https: //github.com/jalemkul/ gmx_tutorials_livecoms; to provide feedback, suggestions, or help improve it, please visit the GitHub repository and participate via the issue tracker. This version dated January 2, 2019 Abstract Molecular dynamics (MD) simulations are a popular technique for studying the atomistic behavior of any molecular system. Performing MD simulations requires a user to become familiar with the commands, options, and file formats of the chosen simulation software, none of which are consistent across different programs. Beyond these requirements, users are expected to be familiar with various aspects of physics, mathematics, computer programming, and interaction with a command-line environment, presenting critical barriers to entry in the MD simulation field. This article presents seven tutorials for instructing users in the proper methods for preparing and carrying out different types of MD simulations in the popular GROMACS simulation package. GROMACS is an open-source, free, and flexible MD package that is consistently among the fastest in the world. The tutorials presented here range from a \"simple\" system of a protein in aqueous solution to more advanced concepts such as force field organization and modification for a membrane-protein system, two methods of calculating free energy differences (umbrella sampling and \"alchemical\" methods), biphasic systems, protein-ligand complexes, and the use of virtual sites in MD simulations. In this article, users are provided the rationale and a theoretical explanation for the command-line syntax in each step in the online tutorials (available at http://www.mdtutorials.com/gmx) and the underlying settings and algorithms necessary to perform robust MD simulations in each scenario.","PeriodicalId":74084,"journal":{"name":"Living journal of computational molecular science","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69480733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 254

Introduction to Markov state modeling with the PyEMMA software [Article v1.0] PyEMMA软件的马尔可夫状态建模简介[第v1.0版]

Living journal of computational molecular science Pub Date : 2019-01-01 DOI: 10.33011/LIVECOMS.1.1.5965

C. Wehmeyer, Martin K. Scherer, Tim Hempel, B. Husic, S. Olsson, F. Noé

引用次数: 43

A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0]. 一套关于WESTPA罕见事件采样软件的教程[文章v1.0]。

Living journal of computational molecular science Pub Date : 2019-01-01 Epub Date: 2019-10-04 DOI: 10.33011/livecoms.1.2.10607

Anthony T Bogetti, Barmak Mostofian, Alex Dickson, A J Pratt, Ali S Saglam, Page O Harrison, Joshua L Adelman, Max Dudek, Paul A Torrillo, Alex J DeGrave, Upendra Adhikari, Matthew C Zwier, Daniel M Zuckerman, Lillian T Chong

引用次数: 16

Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1.0] 分子生物学中的静电建模:DelPhi教程和相关资源[第v1.0条]

Living journal of computational molecular science Pub Date : 2019-01-01 DOI: 10.33011/livecoms.1.2.10841

Shailesh Kumar Panday, Mihiri H. B. Shashikala, Mahesh Koirala, S. Pahari, Arghya Chakrvorty, Yunhui Peng, Lin Li, Zhe Jia, Chuan Li, E. Alexov

{"title":"Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1.0]","authors":"Shailesh Kumar Panday, Mihiri H. B. Shashikala, Mahesh Koirala, S. Pahari, Arghya Chakrvorty, Yunhui Peng, Lin Li, Zhe Jia, Chuan Li, E. Alexov","doi":"10.33011/livecoms.1.2.10841","DOIUrl":"https://doi.org/10.33011/livecoms.1.2.10841","url":null,"abstract":"This LiveCoMS document is maintained online on GitHub at https: //github.com/delphi001/ delphi_tutorial_livecoms; to provide feedback, suggestions, or help improve it, please visit the GitHub repository and participate via the issue tracker. This version dated November 25, 2019 Abstract Electrostatics play an indispensable role in practically any process in molecular biology. Indeed, at distances larger than several Angstroms, all other forces are negligibly small and electrostatic force dominates. However, modeling electrostatics in molecular biology is a complicated task due to presence of water phase, mobile ions and irregularly shaped inhomogeneous biological macromolecules. A particular approach to calculating electrostatics in such systems is to apply the Poisson-Boltzmann equation (PBE). Here, we provide a tutorial for the popular DelPhi package that solves PBE using a finite-difference method and delivers the electrostatic potential distribution throughout the modeling box. The tutorial comes with a detailed description of different tasks that DelPhi can handle, an assessment of the accuracy against cases with analytical solutions and recommendations about DelPhi usage. Furthermore, since electrostatics is a key component of virtually any modeling in molecular biology, we have created many additional resources utilizing DelPhi to model various biology relevant quantities. Tutorials for these resources are also provided along with examples of their usage.","PeriodicalId":74084,"journal":{"name":"Living journal of computational molecular science","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69480794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0]. 双链 DNA 原子模拟的经验教训：溶解和盐问题[文章 v1.0]。

Living journal of computational molecular science Pub Date : 2019-01-01 Epub Date: 2019-08-09 DOI: 10.33011/livecoms.1.2.9974

Rodrigo Galindo-Murillo, Thomas E Cheatham

{"title":"Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0].","authors":"Rodrigo Galindo-Murillo, Thomas E Cheatham","doi":"10.33011/livecoms.1.2.9974","DOIUrl":"10.33011/livecoms.1.2.9974","url":null,"abstract":"Nucleic acids are highly charged macromolecules sensitive to their surroundings of water, salt, and other biomolecules. Molecular dynamics simulations with accurate biomolecular force fields provide a detailed atomistic view into DNA and RNA that has been useful to study the structure and dynamics of these molecules and their biological relevance. In this work we study the Drew-Dickerson dodecamer duplex with the sequence d(GCGCAATTGCGC)2 in three different salt concentrations and using different monvalent salt types to detect possible structural influence. Overall, the DNA shows no major structural changes regardless of amount or type of monovalent ions used. Our results show that only at very high salt conditions (5M) is a small structural effect observed in the DNA duplex, which mainly consist of narrowing of the grooves due to increased residence of ions. We also present the importance of sampling time to achieve a converged ensemble, which is of major relevance in any simulation to avoid biased or non-meaningful results.","PeriodicalId":74084,"journal":{"name":"Living journal of computational molecular science","volume":"1 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7561045/pdf/nihms-1610687.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38505758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0] 计算传输属性的最佳实践平衡分子动力学中的自扩散率和粘度[第v1.0节]

Living journal of computational molecular science Pub Date : 2019-01-01 DOI: 10.33011/LIVECOMS.1.1.6324

E. Maginn, Richard A. Messerly, Daniel J. Carlson, Daniel R. Roe, J. Richard Elliott

引用次数: 142

Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0]. 分子模拟中不确定度和采样质量量化的最佳实践[第v1.0条]。

Living journal of computational molecular science Pub Date : 2018-01-01 Epub Date: 2018-10-27 DOI: 10.33011/livecoms.1.1.5067

Alan Grossfield, Paul N Patrone, Daniel R Roe, Andrew J Schultz, Daniel W Siderius, Daniel M Zuckerman

引用次数: 93