MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
Robert T. McGibbon,Kyle A. Beauchamp,Matthew P. Harrigan,Christoph Klein,Jason M. Swails,Carlos X. Hernández,Christian R. Schwantes,Lee-Ping Wang,Thomas J. Lane,Vijay S. Pande +9 more
TLDR
MDTraj is a modern, lightweight, and fast software package for analyzing MD simulations that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.About:
This article is published in Biophysical Journal.The article was published on 2015-10-20 and is currently open access. It has received 1480 citations till now. The article focuses on the topics: Python (programming language) & Software ecosystem.read more
Citations
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Fast parallel algorithms for short-range molecular dynamics
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
Journal ArticleDOI
Molecular Dynamics Simulation for All.
TL;DR: The types of information molecular dynamics simulations can provide and the ways in which they typically motivate further experimental work are described.
Journal ArticleDOI
PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models.
Martin K. Scherer,Benjamin Trendelkamp-Schroer,Fabian Paul,Guillermo Pérez-Hernández,Moritz Hoffmann,Nuria Plattner,Christoph Wehmeyer,Jan-Hendrik Prinz,Frank Noé +8 more
TL;DR: The open-source Python package PyEMMA is presented, derived a systematic and accurate way to coarse-grain MSMs to few states and to illustrate the structures of the metastable states of the system.
Journal ArticleDOI
Tinker 8: Software Tools for Molecular Design.
Joshua A. Rackers,Zhi Wang,Chao Lu,Marie L. Laury,Louis Lagardère,Michael J. Schnieders,Jean-Philip Piquemal,Pengyu Ren,Jay W. Ponder +8 more
TL;DR: The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions, which supports a wide variety of force fields.
Proceedings ArticleDOI
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations
Richard Gowers,Max Linke,Jonathan Barnoud,Tyler Reddy,Manuel N. Melo,Sean L. Seyler,Jan Domański,David L. Dotson,Sébastien Buchoux,Ian M. Kenney,Oliver Beckstein +10 more
TL;DR: MDAnalysis is a library for structural and temporal analysis of molecular dynamics simulation trajectories and individual protein structures that enables users to rapidly write code that is portable and immediately usable in virtually all biomolecular simulation communities.
References
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Scikit-learn: Machine Learning in Python
Fabian Pedregosa,Gaël Varoquaux,Alexandre Gramfort,Vincent Michel,Bertrand Thirion,Olivier Grisel,Mathieu Blondel,Peter Prettenhofer,Ron Weiss,Vincent Dubourg,Jake Vanderplas,Alexandre Passos,David Cournapeau,Matthieu Brucher,Matthieu Perrot,Edouard Duchesnay +15 more
TL;DR: Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems, focusing on bringing machine learning to non-specialists using a general-purpose high-level language.
Journal ArticleDOI
VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Journal ArticleDOI
Fast parallel algorithms for short-range molecular dynamics
TL;DR: In this article, three parallel algorithms for classical molecular dynamics are presented, which can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors.
Fast parallel algorithms for short-range molecular dynamics
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
Posted Content
Scikit-learn: Machine Learning in Python
Fabian Pedregosa,Gaël Varoquaux,Alexandre Gramfort,Vincent Michel,Bertrand Thirion,Olivier Grisel,Mathieu Blondel,Andreas Müller,Joel Nothman,Gilles Louppe,Peter Prettenhofer,Ron Weiss,Vincent Dubourg,Jake Vanderplas,Alexandre Passos,David Cournapeau,Matthieu Brucher,Matthieu Perrot,Edouard Duchesnay +18 more
TL;DR: Scikit-learn as mentioned in this paper is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems.