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Abstract
The typical workflow in molecular dynamics (MD) analysis requires several separate tools, often resulting in a lack of synergy and interaction between the individual analysis steps. In this seminar, we will present VIAMD [1] (https://github.com/scanberg/viamd) , an application designed to address this issue by integrating a 3D visualization of molecular trajectories with flexible analysis components. VIAMD uses an interactive scripting interface, allowing for property definition and evaluation. The application provides context-aware suggestions and expression feedback through information and visualizations. The user-defined properties can be explored and analyzed through the various components. This enables correlation with spatial conformations, statistical analysis of distributions, and powerful aggregation of multidimensional properties such as spatial distribution functions. We would be happy to use data from the participants for the webinar, so contact us if you are willing to share your data with us.
[1] Skånberg et al., J. Chem. Inf. Model. 2023, 63, 23, 7382–7391 (2023)
Presenters
Robin Skånberg is a PhD student in the group of Scientific Visualization at the Media and Information Technology (LIU, Linköping, Sweden). His main research focus is developing techniques for molecular visualization used for software development (VIAMD) and immersive visualization. The molecular datasets he works with can originate from simulations, x-ray crystallography, or cryo-EM. Robin is the lead developer of VIAMD.
Contact: robin.skanberg@liu.se
Mathieu Linares is an application expert at the PDC supercomputer center (KTH, Stockholm, Sweden). He received his PhD degree from Paul Cézanne University, Marseille, France, in 2005. His research activities have been focusing on self-assembly, chirality, organic electronics, and protein-molecule interaction. From 2018 to June 2023, he held an associate professor position in the Group of Scientific Visualization at Linköping University, helping bridge the gap between theoretical chemistry and scientific visualization and leading to the development of VIAMD.
Contact: linares@kth.se
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