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Visualization Tools for Computational Chemistry

PDC lunchtime seminar

Come and learn about new visualization tools for computational chemistry! There will also be an opportunity after the seminar to try out these tools for your own data.

Time: Tue 2023-09-19 12.00 - 13.00

Location: SeRC room, Level 5, PDC, KTH, Teknikringen 14, 114 28 Stockholm

Video link:

Language: English

Participating: Mathieu Linares, PDC


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In this seminar, Mathieu will present the latest visualization tools that he and his colleagues have been developing for both Molecular Dynamics (MD) and Quantum Chemistry (QM).

Firstly, Mathieu will introduce VIAMD [1,2], a visualization tool designed for the exploration of large-scale spatio-temporal molecular dynamics simulation data. VIAMD enables users to visually analyse and explore molecular dynamics simulations by offering an interactive scripting interface. This interface allows users to define and evaluate properties of interest. The application also provides context-aware suggestions and feedback on expressions, including type information and visualizations. By utilising the various components of VIAMD, users can explore and analyse user-defined properties, allowing for correlation with spatial conformations, statistical analysis of distributions, and powerful aggregation of multidimensional properties such as Spatial Distribution Functions.

Secondly, Mathieu will present VALET [3,4], a Python library specifically developed for the analysis of orbitals in molecules and molecular complexes within Quantum Chemistry. VALET supports the computation of electronic charges and charge transfer during electronic transitions at both the molecular and subgroup levels.

During the presentation, Mathieu will provide a demonstration of both tools. Additionally, interested potential users are invited to stay after the presentation with their datasets to try out VIAMD and VALET. For those interested in using VIAMD, please bring a trajectory file, preferably in the GROMACS (GRO+XTC) or PDB format, and for VALET, please bring a pair of orbitals to compare, such as a pair of hole and particle Natural Transition Orbitals (NTO) from an electronic excitation.


  1. R Skånberg, I Hotz, A Ynnerman, M. Linares "VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics", J. Chem. Inf. Model., 2023, under revision
  3. Masood, T.B., Thygesen, S., Linares, M., Abrikosov, A.I., Natarajan, V. and Hotz, I. "Visual Analysis of Electronic Densities and Transitions in Molecules", Computer Graphics Forum, 2021, 40: 287-298


A light lunch (sandwiches) will be provided for participants. If you will attend the seminar in person, you are required to register at the following link:  so catering can be planned accordingly.

Note: Registration closes on Friday the 15th of September.