Other software

There are some software tools, like visuals and GUI’s, that can be in principle put into the container, however, piping the software to an output is challenging and needs extended skills in terminal programming. Hence, for these software, we recomment to install them as application following their online installation description.

The softwares, that fall into this classification, are:

  • VESTA

  • VMD

VESTA

VESTA (Visualization for Electronic and Structural Analysis) is software designed for visualizing and analyzing the crystal structures, volumetric data, and electronic states of materials. It supports a wide variety of data formats, enabling users to view and manipulate crystal structures, atomic coordinates, electron densities, and isosurfaces. VESTA is widely used in materials science and solid-state chemistry due to its ability to generate high-quality, customizable 3D models, which aid in studying the structural and electronic properties of materials. It also features tools for symmetry analysis, creating polyhedra, and plotting charge density.

The offical website is here .

VMD

VMD (Visual Molecular Dynamics) is software used for molecular modeling, visualization, and analysis of biological systems, including proteins, nucleic acids, and lipid bilayers. It allows researchers to visualize molecular structures and simulate interactions over time, typically in conjunction with molecular dynamics software like LAMMPS, NAMD, or GROMACS. VMD supports various visualization styles (e.g., ribbons, surfaces, space-filling) and provides tools for analyzing molecular dynamics simulations, including calculating properties, rendering high-quality graphics, and scripting for custom analyses. This makes it essential for research in molecular biology, biophysics, and materials science.

The offical website is here .

Although we aimed for registration free softwares in the course, it is unfortunately needed to register for VMD.

Note that VMD brings its own terminal when you open it. There will be some commands that we have to run in the VMD terminal.