VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics

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. This article presents 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. VIAMD has the potential to advance research in many scientific disciplines and is a promising solution for improving the workflow of MD visualization and analysis.

Ultralight aerogels via supramolecular polymerization of a new chiral perfluoropyridine-based sulfonimidamide organogelator

“…5F). In addition, the concentration-dependence of the monomer was measured using 19 F NMR spectroscopy upon 83 dilution of the total concentration at a fixed temperature (293 Fig. Both the temperature-and concentration-dependent curves show the shape of sharp transitions from monomers to an aggregated structure that is the hallmark of a cooperative polymerization mechanism.…”

“…(E & F) Fiber thickness, observed from different view angles. All illustrations and MD trajectory analyses were performed with the VIAMD software 83.…”

Tuning the Emission of Bis-ethylenedioxythiophene-thiophenes upon Aggregation

“…For the production run, the temperature of the system was kept constant at 300 K with a pressure at 1 atm for 100 ns with a step of 2 fs. Visualization of MD data was done with VIAMD software …”

Computation of X-ray and Neutron Scattering Patterns to Benchmark Atomistic Simulations against Experiments

“…The requirement for speed restricts the choice to the latter two [43], and if not only amorphous systems are to be studied, only Sassena remains. In contrast to Sassena, LiquidLib and MDANSE can also calculate other quantities from the simulations, but there are also many other software options like VMD [44,45], MDAnalysis [46,47], TRAVIS [48,49], or viamd [50] for this purpose. The focus of this work is therefore the calculation of neutron and X-ray scattering patterns using and enhancing Sassena.…”