Visual Interactive Analysis of Molecular Dynamics
VIAMD is an interactive analysis tool for molecular dynamics (MD) written in C/C++. VIAMD is developed at the PDC Center for High Performance Computing (KTH, Stockholm). It exposes a rudimentary scripting language for declaring operations performed across trajectory frames. The results can then be viewed in the different windows exposed in the application.
For Windows, we recommend using the latest binary available on the release page.
For macOS, we recommend using the latest binary available on the release page.
NOTE: To be able to run this, you will have to do some magic in a terminal to be able to run the app bundle since we do not have code signing.
xattr -dr com.apple.quarantine viamd.app
To build VIAMD on your machine, you can follow the procedure described in detail in the wiki for Linux and MacOS.
Documentation about VIAMD is available on the github wiki. The first two chapters relate to the visual and analysis features, respectively, where we highlight the interactive part of the software. The third chapter focuses on the VIAMD language used for scripting, and the fourth chapter proposes a series of tutorial (under construction).
A series of videos is available on youtube.
If you want to stay informed about the latest updates of VIAMD, please register your email address on the form.
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General Framework:
- R Skånberg, I Hotz, A Ynnerman, M Linares, VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics, J. Chem. Inf. Model. 2023, 63, 23, 7382–7391 https://doi.org/10.1021/acs.jcim.3c01033
- R Skånberg, C König, P Norman, M Linares, D Jönsson, I Hotz, A Ynnerman, VIA-MD: Visual Interactive Analysis of Molecular Dynamics, 2018, Eurographics Proceedings, p. 19–27
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Specific tool:
- Selection tool: Robin Skånberg, Mathieu Linares, Martin Falk, Ingrid Hotz, Anders Ynnerman, MolFind-Integrated Multi-Selection Schemes for Complex Molecular Structures, 2019, The Eurographics Association, p. 17-21
- Shape Space and Spatial Distribution Function: Robin Skånberg, Martin Falk, Mathieu Linares, Anders Ynnerman, Ingrid Hotz, Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions, 2021, IEEE Transactions on Visualization and Computer Graphics, 28 (9), 3126-3137
- VIAMD has received financial support since 2018 from the Swedish e-Research center (SeRC) and the Wallenberg Foundation
- VIAMD is currently supported as a development project in InfraVis
https://github.com/dougbinks/enkiTS
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https://github.com/epezent/implot
https://github.com/BalazsJako/ImGuiColorTextEdit
https://github.com/skaslev/gl3w
https://github.com/max0x7ba/atomic_queue
https://github.com/mlabbe/nativefiledialog
https://github.com/nothings/stb
