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PDC Center for High Performance Computing

VIAMD Update

Mathieu Linares, PDC

Since the publication of an article in November 2023 which presented the VIAMD code (“VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics” – see doi.org/10.1021/acs.jcim.3c01033 ), the VIAMD development team have implemented several new features including handling of trajectories from the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular dynamics program and new functionality to extract, calculate and plot coordinates and densities across a box as exemplified on the ion-conducting membrane shown above.

The team is currently working on adding support for VeloxChem files to VIAMD in order to efficiently evaluate and render molecular orbitals under different modalities, making it possible, for instance, to undertake interactive analysis of absorption spectra of large molecular systems in terms of natural transition orbitals.

When it comes to dissemination, the team has created a range of tutorial videos that are available on a YouTube playlist ( bit.ly/4aRsPrh ) and an X account: @VIAMD_( x.com/VIAMD_ ). If you would like to start using VIAMD, you can find it on Github ( github.com/scanberg/viamd ).

Illustration of the new functionalities in VIAMD for calculating and plotting coordinates and densities across a box as exemplified on a sodium channel (Dataset courtesy of Lucie Delemotte’s Lab, Science for Life Lab/KTH)