VIAMD

Visual Interactive Analysis of Molecular Dynamics

VIAMD is an interactive analysis tool for molecular dynamics (MD) written in C/C++. VIAMD is developed in collaboration with the Department for Media and Information Technology (LIU, Norrköping) and the PDC Center for High Performance Computing (KTH, Stockholm). It exposes a rudementary script language that is used to declare operations which are performed over the frames of the trajectory. The results can then be viewed in the different windows exposed in the application.

Status

Running VIAMD

Windows

For windows, we recommend to use the latest binary available on the release page.

Ubuntu and MacOs

To build VIAMD on your machine, you can follow the procedure described in details in the wiki for Linux and MacOS.

Documentation

Documentation about VIAMD is available on the github wiki. The two first chapters relate to the visual and analysis features respectively, where we highlight the interactive part of software. The third chapter focus on the VIAMD language used for scripting and the fourth chapter propose a serie of tutorial (under construction).

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:

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

Financial Support

VIAMD has received constant financial support since 2018 from the Swedish e-Research center (SeRC) and the Wallenberg Foundation

VIAMD is supported by InfraVis for specific projets:

Parser for LAMMPS file (2301-5217 / 140 hours)
Interactice analysis of VeloxChem file (interactive analysis of orbitals and spectra plotting) (600 hours)