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Sol Login Node
Known Issue: These On the Sol login node, these tools work only when connecting from a Linux box. Users have reported different error messages when logging in from a Mac and we haven't found a resolution. If you need to use these visualization tools, please login from a linux machine.
Avogadro
Avogadro is a molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Features
- Molecular builder-editor for Windows, Linux, and OS X.
- All source code is licensed under the GNU GPL.
- Translations into Chinese, French, German, Italian, Russian, and Spanish.
- Supports multi-threaded rendering and computation.
- Plugin architecture for developers, including rendering, interactive tools, commands, and Python scripts.
- OpenBabel import of files, input generation for multiple computational chemistry packages, crystallography, and biomolecules.
Useful Links
GaussView
GaussView is a graphical interface used with Gaussian. It aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output (e.g., you can use it to plot properties, animate vibrations, visualize computed spectra, etc.).
Useful Links
GNUplot
Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave.
Useful Links
ParaView
ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.
ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of petascale size as well as on laptops for smaller data, has become an integral tool in many national laboratories, universities and industry, and has won several awards related to high performance computation.
Useful Links
PWGui
PWgui is a GUI for PWscf based programs from Quantum-ESPRESSO integrated suite of codes for electronic structure calculations and materials modeling at the nanoscale.
PyMol
A molecular visualization system on an open source foundation, maintained and distributed by Schrödinger
VESTA
VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. Some of the novel features of VESTA are listed below.
- Deal with multiple structural models, volumetric data, and crystal morphologies in the same window.
- Support multiple tabs corresponding to files.
- Support multiple windows with more than two tabs in the same process.
- Deal with virtually unlimited number of objects such as atoms, bonds polyhedra, and polygons on isosurfaces (theoretical limit on 32bit operating system is 1,073,741,823)
- Support lattice transformation from conventional to non-conventional lattice by using matrix. The transformation matrix is also used to create superlattice and sublattice.
- Visualize interatomic distances and bond angles that are restrained in Rietveld analysis with RIETAN-FP.
- Transparent isosurfaces can be overlap with structural models.
- Isosurface can be colored on the basis of another physical quantity.
- Arithmetic operations among multiple volumetric data files.
- High quality smooth rendering of isosurfaces and sections.
- Export high-resolution graphic images exceeding Video card limitation.
VMD
Visual Molecular Dynamics (VMD) is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
XCrySDen
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Open OnDemand
The following tools are available as an Interactive App on the Open OnDemand HPC Portal.