Living journal of computational molecular science最新文献_第2页

A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0]. 琥珀和 CHARMM 中的连续恒定 pH 值分子动力学方法指南[文章 v1.0]。

Living journal of computational molecular science Pub Date : 2022-01-01 Epub Date: 2022-08-22 DOI: 10.33011/livecoms.4.1.1563

Jack A Henderson, Ruibin Liu, Julie A Harris, Yandong Huang, Vinicius Martins de Oliveira, Jana Shen

引用次数: 0

How To Be a Good Member of a Scientific Software Community [Article v1.0]. 如何成为科学软件社区的好成员[文章v1.0]。

Living journal of computational molecular science Pub Date : 2021-08-31 DOI: 10.31219/osf.io/kgr45

A. Grossfield

引用次数: 2

Trends in atomistic simulation software usage [Article v1.0] 原子模拟软件的使用趋势[第v1.0篇]

Living journal of computational molecular science Pub Date : 2021-08-27 DOI: 10.33011/livecoms.3.1.1483

Leopold Talirz, L. Ghiringhelli, B. Smit

引用次数: 7

How To Be a Good Member of a Scientific Software Community [Article v1.0]. 如何成为科学软件社区的好成员[文章v1.0]。

Living journal of computational molecular science Pub Date : 2021-01-01 DOI: 10.33011/livecoms.3.1.1473

Alan Grossfield

引用次数: 2

Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]. 用分子模拟解释氢-氘交换实验：HDXer集成重加权软件的教程和应用[第v1.0版]。

Living journal of computational molecular science Pub Date : 2021-01-01 Epub Date: 2022-01-26 DOI: 10.33011/livecoms.3.1.1521

Paul Suhwan Lee, Richard T Bradshaw, Fabrizio Marinelli, Kyle Kihn, Ally Smith, Patrick L Wintrode, Daniel J Deredge, José D Faraldo-Gómez, Lucy R Forrest

{"title":"Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0].","authors":"Paul Suhwan Lee, Richard T Bradshaw, Fabrizio Marinelli, Kyle Kihn, Ally Smith, Patrick L Wintrode, Daniel J Deredge, José D Faraldo-Gómez, Lucy R Forrest","doi":"10.33011/livecoms.3.1.1521","DOIUrl":"10.33011/livecoms.3.1.1521","url":null,"abstract":"Hydrogen-deuterium exchange (HDX) is a comprehensive yet detailed probe of protein structure and dynamics and, coupled to mass spectrometry, has become a powerful tool for investigating an increasingly large array of systems. Computer simulations are often used to help rationalize experimental observations of exchange, but interpretations have frequently been limited to simple, subjective correlations between microscopic dynamical fluctuations and the observed macroscopic exchange behavior. With this in mind, we previously developed the HDX ensemble reweighting approach and associated software, HDXer, to aid the objective interpretation of HDX data using molecular simulations. HDXer has two main functions; first, to compute H-D exchange rates that describe each structure in a candidate ensemble of protein structures, for example from molecular simulations, and second, to objectively reweight the conformational populations present in a candidate ensemble to conform to experimental exchange data. In this article, we first describe the HDXer approach, theory, and implementation. We then guide users through a suite of tutorials that demonstrate the practical aspects of preparing experimental data, computing HDX levels from molecular simulations, and performing ensemble reweighting analyses. Finally we provide a practical discussion of the capabilities and limitations of the HDXer methods including recommendations for a user's own analyses. Overall, this article is intended to provide an up-to-date, pedagogical counterpart to the software, which is freely available at https://github.com/Lucy-Forrest-Lab/HDXer.","PeriodicalId":74084,"journal":{"name":"Living journal of computational molecular science","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9835200/pdf/nihms-1830743.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9236261","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

A Suite of Advanced Tutorials for the GROMOS Biomolecular Simulation Software [Article v1.0] GROMOS生物分子模拟软件高级教程[第v1.0条]

Living journal of computational molecular science Pub Date : 2020-01-01 DOI: 10.33011/livecoms.2.1.18552

Niels Hansen, Christoph Öehlknecht, Anita de Ruiter, Bettina Lier, W. V. van Gunsteren, C. Oostenbrink, J. Gebhardt

引用次数: 4

Best Practices for Alchemical Free Energy Calculations [Article v1.0]. 炼金术自由能计算的最佳实践[第v1.0条]。

Living journal of computational molecular science Pub Date : 2020-01-01 DOI: 10.33011/2.1.18378

A. Mey, Bryce K. Allen, H. B. Macdonald, J. Chodera, David F. Hahn, M. Kuhn, J. Michel, D. Mobley, Levi N. Naden, Samarjeet Prasad, A. Rizzi, Jenke Scheen, M. Shirts, G. Tresadern, Huafeng Xu

{"title":"Best Practices for Alchemical Free Energy Calculations [Article v1.0].","authors":"A. Mey, Bryce K. Allen, H. B. Macdonald, J. Chodera, David F. Hahn, M. Kuhn, J. Michel, D. Mobley, Levi N. Naden, Samarjeet Prasad, A. Rizzi, Jenke Scheen, M. Shirts, G. Tresadern, Huafeng Xu","doi":"10.33011/2.1.18378","DOIUrl":"https://doi.org/10.33011/2.1.18378","url":null,"abstract":"Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of \"bridging\" potential energy functions representing alchemical intermediate states that cannot exist as real chemical species. The data collected from these bridging alchemical thermodynamic states allows the efficient computation of transfer free energies (or differences in transfer free energies) with orders of magnitude less simulation time than simulating the transfer process directly. While these methods are highly flexible, care must be taken in avoiding common pitfalls to ensure that computed free energy differences can be robust and reproducible for the chosen force field, and that appropriate corrections are included to permit direct comparison with experimental data. In this paper, we review current best practices for several popular application domains of alchemical free energy calculations performed with equilibrium simulations, in particular relative and absolute small molecule binding free energy calculations to biomolecular targets.","PeriodicalId":74084,"journal":{"name":"Living journal of computational molecular science","volume":"2 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69480723","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: 123

Best Practices for Alchemical Free Energy Calculations [Article v1.0]. 炼金术自由能计算的最佳实践[第v1.0条]。

Living journal of computational molecular science Pub Date : 2020-01-01 DOI: 10.33011/livecoms.2.1.18378

Antonia S J S Mey, Bryce K Allen, Hannah E Bruce Macdonald, John D Chodera, David F Hahn, Maximilian Kuhn, Julien Michel, David L Mobley, Levi N Naden, Samarjeet Prasad, Andrea Rizzi, Jenke Scheen, Michael R Shirts, Gary Tresadern, Huafeng Xu

{"title":"Best Practices for Alchemical Free Energy Calculations [Article v1.0].","authors":"Antonia S J S Mey, Bryce K Allen, Hannah E Bruce Macdonald, John D Chodera, David F Hahn, Maximilian Kuhn, Julien Michel, David L Mobley, Levi N Naden, Samarjeet Prasad, Andrea Rizzi, Jenke Scheen, Michael R Shirts, Gary Tresadern, Huafeng Xu","doi":"10.33011/livecoms.2.1.18378","DOIUrl":"https://doi.org/10.33011/livecoms.2.1.18378","url":null,"abstract":"Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of \"bridging\" potential energy functions representing alchemical intermediate states that cannot exist as real chemical species. The data collected from these bridging alchemical thermodynamic states allows the efficient computation of transfer free energies (or differences in transfer free energies) with orders of magnitude less simulation time than simulating the transfer process directly. While these methods are highly flexible, care must be taken in avoiding common pitfalls to ensure that computed free energy differences can be robust and reproducible for the chosen force field, and that appropriate corrections are included to permit direct comparison with experimental data. In this paper, we review current best practices for several popular application domains of alchemical free energy calculations performed with equilibrium simulations, in particular relative and absolute small molecule binding free energy calculations to biomolecular targets.","PeriodicalId":74084,"journal":{"name":"Living journal of computational molecular science","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8388617/pdf/nihms-1717408.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10237667","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: 110

Lessons Learned from the Calculation of One-Dimensional Potentials of Mean Force [Article v1.0] 从平均力的一维势能计算中吸取的经验教训[第v1.0条]

Living journal of computational molecular science Pub Date : 2019-11-22 DOI: 10.33011/livecoms.1.2.11073

Daniel Markthaler, S. Jakobtorweihen, Niels Hansen

{"title":"Lessons Learned from the Calculation of One-Dimensional Potentials of Mean Force [Article v1.0]","authors":"Daniel Markthaler, S. Jakobtorweihen, Niels Hansen","doi":"10.33011/livecoms.1.2.11073","DOIUrl":"https://doi.org/10.33011/livecoms.1.2.11073","url":null,"abstract":"The origins of different computational artifacts that may occur in the calculation of one-dimensional potentials of mean force (PMF) via umbrella sampling molecular dynamics simulations and manifest as free energy offset between bulk solvent regions are investigated. By systematic studies, three distinct causes are elucidated: (i) an unfortunate choice of reference points for the umbrella distance restraint; (ii) a misfit in probability distributions between bound and unbound umbrella windows in case of multiple binding modes; (iii) artifacts introduced by the free energy estimator. Starting with a fully symmetric model system consisting of methane binding to a cylindrical host, complexity is increased through the introduction of dipolar interactions between the host and the solvent, the host and the guest molecule or between all involved species, respectively. The manifestation of artifacts is illustrated and their origin and prevention is discussed. Finally, the consequences for the calculation of standard binding free enthalpies is illustrated using the complexation of primary alcohols with alpha-cyclodextrin as an example.","PeriodicalId":74084,"journal":{"name":"Living journal of computational molecular science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49592408","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: 6

Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0] 提高Tinker-HP分子建模包的性能[第v1.0条]

Living journal of computational molecular science Pub Date : 2019-06-04 DOI: 10.33011/livecoms.1.2.10409

Luc-Henri Jolly, A. Duran, Louis Lagardère, J. Ponder, P. Ren, Jean‐Philip Piquemal

{"title":"Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0]","authors":"Luc-Henri Jolly, A. Duran, Louis Lagardère, J. Ponder, P. Ren, Jean‐Philip Piquemal","doi":"10.33011/livecoms.1.2.10409","DOIUrl":"https://doi.org/10.33011/livecoms.1.2.10409","url":null,"abstract":"This living paper reviews the present High Performance Computing (HPC) capabilities of the Tinker-HP molecular modeling package. We focus here on the reference, double precision, massively parallel molecular dynamics engine present in Tinker-HP and dedicated to perform large scale simulations. We show how it can be adapted to recent Intel Central Processing Unit (CPU) petascale architectures. First, we discuss the new set of Intel Advanced Vector Extensions 512 (Intel AVX-512) instructions present in recent Intel processors (e.g., the Intel Xeon Scalable and Intel Xeon Phi 2nd generation processors) allowing for larger vectorization enhancements. These instructions constitute the central source of potential computational gains when using the latest processors, justifying important vectorization efforts for developers. We then briefly review the organization of the Tinker-HP code and identify the computational hotspots which require Intel AVX-512 optimization and we propose a general and optimal strategy to vectorize those particular parts of the code. We intended to present our optimization strategy in a pedagogical way so it could benefit to other researchers and students interested in gaining performances in their own software. Finally we present the performance enhancements obtained compared to the unoptimized code both sequentially and at the scaling limit in parallel for classical non-polarizable (CHARMM) and polarizable force fields (AMOEBA). This paper never ceases to be updated as we accumulate new data on the associated Github repository between new versions of this living paper.","PeriodicalId":74084,"journal":{"name":"Living journal of computational molecular science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46093416","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: 8