Jmol simulation software#

XCrySDen (X-window CRYstalline Structures and DENsities) VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. VESTA (Visualization for Electronic and STructure Analysis)

Jmol simulation software#

OVITO is a scientific visualization and analysis software for atomistic simulation data. Open RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. GDIS is a scientific visualization program for the display, manipulation, and analysis of isolated molecules and periodic structures.

TopoTools is a VMD plugin for manipulating topology information.ĪtomEye is an atomistic configuration viewer.ĪViz (Atomistic Simulation Vizualization software)ĭdplot visualizes dislocations in crystals using the so-called differential displacement maps. Pizza.py is a loosely integrated collection of tools, many of which provide pre- and post-processing capability for the LAMMPS molecular dynamics, ChemCell cell modeling, and SPPARKS kinetic Monte Carlo packages. The packing guarantees that short range repulsive interactions do not disrupt the simulations. Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. NanoSCULPT is a tool/methodology to generate complex and realistic structures for atomistic simulations. It is typically used for building coarse-grained toy molecular models. Moltemplate is a cross-platform text-based molecule builder for LAMMPS. The focus of the package is to facilitate the rapid design and development of simulations that are fully documented and easily adaptable to new potentials/atomic arrangements/etc.ĪSE provides Python modules for manipulating atoms, analyzing simulations, visualization etc.Īvogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.Ī Fortran program to insert dislocation in atomistic simulations, calculate their elastic energy, extract the Nye tensors, and much more.ĬIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis.Īten is a tool to create, edit, and visualise coordinates.ĪtomMan: the Atomistic Manipulation Toolkit is a Python library for interacting with large-scale atomic systems. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. Below is a list of other codes that can create, transform, visualize, and/or convert files for atomic systems. The complete documentation of Atomsk (headless)Ītomsk is not alone! A lot of very useful tools exist out there.