mdanalysis.org

MDAnalysis · MDAnalysis

A Python package for the analysis of molecular dynamics simulations. Is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections. Suitable for visualization or native analysis tools. MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the PDB format) and access the atomic coordinates through NumPy.

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MDAnalysis · MDAnalysis | mdanalysis.org Reviews

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A Python package for the analysis of molecular dynamics simulations. Is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections. Suitable for visualization or native analysis tools. MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the PDB format) and access the atomic coordinates through NumPy.

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MDAnalysis · MDAnalysis | mdanalysis.org Reviews

https://mdanalysis.org

A Python package for the analysis of molecular dynamics simulations. Is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections. Suitable for visualization or native analysis tools. MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the PDB format) and access the atomic coordinates through NumPy.

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mdanalysis.org

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Learning MDAnalysis · MDAnalysis

http://www.mdanalysis.org/pages/learning_MDAnalysis

A Python package for the analysis of molecular dynamics simulations. Once you had a look at the basic example. You might want to learn more about how to use MDAnalysis. MDAnalysis is primarily a library that helps you to build your own tools but it also works very well for interactive data exploration. Of MD data in IPython. In particular within Jupyter notebooks. And in conjunction with pandas. MDAnalysis is well suited for a. Serves as an introduction to the library and there are other tutorials.

2

Blog · MDAnalysis

http://www.mdanalysis.org/blog

A Python package for the analysis of molecular dynamics simulations. Google Summer of Code 2017. MDAnalysis has been accepted as a sub-org. Foundation, for Google Summer of Code 2017. If you are interested in working with us this summer as a student read the advice and links below and write to us on the mailing list. We are looking forward to all applications from interested students (. The application window deadline. Is April 3, 2017 at 12:00 (MST). As soon as possible. And we can discuss it there.

3

Citations · MDAnalysis

http://www.mdanalysis.org/pages/citations

A Python package for the analysis of molecular dynamics simulations. When using MDAnalysis in published work, please cite the following two papers:. R J Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S Benthall and S. Rostrup, editors,. Proceedings of the 15th Python in Science Conference. J Comput. Chem. J Biomol. St...

4

About MDAnalysis · MDAnalysis

http://www.mdanalysis.org/about

A Python package for the analysis of molecular dynamics simulations. Is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM. It also reads other formats (e.g. PDB. Files and XYZ format. Trajectories; see the supported coordinate formats. For the full list). It can write most of these formats, too, together with atom selections for use in Gromacs. MDAnalysis allows one to read molecular dynamics trajectories and access the atomic coordinates through NumPy.

5

Basic example · MDAnalysis

http://www.mdanalysis.org/pages/basic_example

A Python package for the analysis of molecular dynamics simulations. A typical usage pattern is to iterate through a trajectory and analyze coordinates for every frame. In the following example the end-to-end distance of a protein and the radius of gyration of the backbone atoms are calculated:. Always start with a Universe. Can access via segid (s4AKE) and atom name. Takes the last atom named 'C'. Iterate through all frames. End-to-end vector from atom positions. Frame = {0}: d = {1} A, Rgyr = {2} A".

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Software — SPIDAL 1.0 documentation

http://www.spidal.org/software.html

SPIDAL Project on ResearchGate. Launch of Intelligent Systems Engineering - Fall 2016. 450,000 Navy grant fuels IU-NSWC Crane effort. IU an Intel Parallel Computing Center. Kansas, Crandall collaborate on 3-D imaging. Qiu named Outstanding Junior Faculty. DIBBS progam and SPIDAL news. Madhav V. Marathe. Analytics of Three-Dimensional Pathology Imaging Data. Computer Vision Meets High-Performance Computing. 3D Surface Extraction update. Identifying HPC-ABDS Software Stack. HARP: A HADOOP PLUG-IN. SPATIAL ...

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Project "mdanalysis" has moved to another location on the Internet. View the project at: http:/ www.mdanalysis.org. For pages about "mdanalysis". If you are the project's administrator, you can update the new project URL here. Powered by Google Project Hosting.

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Publications — SPIDAL 1.0 documentation

http://www.spidal.org/bib.html

SPIDAL Project on ResearchGate. Launch of Intelligent Systems Engineering - Fall 2016. 450,000 Navy grant fuels IU-NSWC Crane effort. IU an Intel Parallel Computing Center. Kansas, Crandall collaborate on 3-D imaging. Qiu named Outstanding Junior Faculty. DIBBS progam and SPIDAL news. Madhav V. Marathe. Analytics of Three-Dimensional Pathology Imaging Data. Computer Vision Meets High-Performance Computing. 3D Surface Extraction update. Identifying HPC-ABDS Software Stack. HARP: A HADOOP PLUG-IN. SPATIAL ...

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MDAnalysis · MDAnalysis

A Python package for the analysis of molecular dynamics simulations. Is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections. Suitable for visualization or native analysis tools. MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the PDB format) and access the atomic coordinates through NumPy.

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