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mathieulinares edited this page Feb 27, 2024 · 36 revisions

About

VIAMD is developed in the Department for Media and Information Technology (LIU, Norrköping). It allows a visual exploration of large-scale spatio-temporal molecular dynamics simulation data.

overview_2

After loading a trajectory, you can navigate through it using the animation window. Using the script editor and VIAMD language, one can derive a series of geometrical parameters for a molecule or an ensemble of molecules. This parameters can then be followed in the timeline and distribution window.

By using the filtering in the timeline, you can compare your distribution for the full trajectory and for the filtered part of your trajectory.

To illustrate the functionalities of VIAMD, this manual will used as examples three datasets: (A) a multiple PDB file of a poly-alanine chain; (B) A Gromacs trajectory of an aspirin molecule being pulled out of its specific binding to Phospholipase A2. The dynamic was performed from the crystal structure (1OXR) of the complex (C) a gromacs trajectory of luminescent probes in interaction with AB-amyloid. (More details in the dataset section)

A series of videos is available on youtube.

Update

If you want to stay informed about the latest update of VIAMD, please register your email address to the form.

Citations

If you are using VIAMD for your research, please cite the following article:

  • 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

  • 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​

This is the VIAMD logo

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