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Dear all,

You are cordially invited to the PDC-SeRC lunch Seminar that will take place the 19th of September from 12:00 to 13:00 in the SeRC room at level 5, PDC, KTH, Teknikringen 14, 114 28 Stockholm.

We will provide sandwiches to participants, you are therefore required to register at the following link so we can plan accordingly:

Speaker: Mathieu Linares, PDC, Center for High Performance Computing
Title: Visualization Tools for Computational Chemistry

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

Firstly, I 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 analyze 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 utilizing the various components of VIAMD, users can explore and analyze 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, I 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, I 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. As 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