What is a CUBE file?
CUBE file format, also known as Gaussian Cube file (.cube) is used in computational chemistry for storing molecular data, particularly electron density information resulting from quantum chemistry calculations. This format is commonly associated with Gaussian software package, which is widely used for performing ab initio electronic structure calculations.
Gaussian Cube files store three-dimensional data, typically representing electron density or other properties of molecules, obtained through quantum chemistry calculations. The file contains header section with metadata (such as origin, number of data points along each axis, and spacing), followed by grid of numerical values representing property of interest (e.g., electron density) at each grid point in space.
Gaussian Cube file (.cube) is a plain-text file with specific structure. The header contains information about molecular system and data grid, and data values are arranged in three-dimensional grid format. Gaussian Cube files are often used to visualize molecular properties using molecular visualization software. Programs like VMD (Visual Molecular Dynamics) or PyMOL can read Gaussian Cube files to display molecular surfaces, electron density, or other calculated properties.
Simplified example of Gaussian Cube file:
Cubefile Example
Generated by Gaussian
0 1 0 0 0 0 0 0 0 0
0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00
50 0.1000000000000000E+01 0.0000000000000000E+00 0.0000000000000000E+00
50 0.0000000000000000E+00 0.1000000000000000E+01 0.0000000000000000E+00
50 0.0000000000000000E+00 0.0000000000000000E+00 0.1000000000000000E+01
0.123456789E+02 0.123456789E+02 0.123456789E+02 0.123456789E+02 0.123456789E+02
... (data values for electron density at each grid point)
About Gaussian
Gaussian is a suite of software applications for quantum chemistry and computational chemistry. The primary focus of Gaussian is on ab initio quantum chemistry methods, which are highly accurate but computationally intensive approaches to studying electronic structure of molecules. The software is widely used in research and academic settings for various applications, including predicting molecular properties, studying reaction mechanisms, and exploring molecular structures.
About NWChem
NWChem is an open-source computational chemistry software designed for high-performance quantum chemistry simulations. It employs ab initio methods such as Hartree-Fock and density functional theory, supports parallel computing for efficient calculations on clusters, and finds applications in diverse scientific fields, including computational chemistry, biochemistry, and materials science. NWChem is known for its versatility, allowing researchers to study various chemical systems, and its open-source nature encourages community contributions and customization.
About VMD
VMD, which stands for Visual Molecular Dynamics, is powerful and widely used molecular visualization program for displaying, analyzing, and animating molecular dynamics (MD) trajectories, as well as static molecular structures. It is particularly popular in fields of computational chemistry, molecular biology, and structural bioinformatics. VMD excels at visualizing molecular structures, providing high-quality 3D renderings of molecules and molecular complexes. It supports variety of molecular file formats.
About PyMOL
PyMOL is a molecular visualization system and software tool used for three-dimensional visualization of molecular structures. It is particularly popular in fields of structural biology, bioinformatics, and computational chemistry. PyMOL provides high-quality 3D renderings of molecular structures, enabling users to visualize and explore shapes, surfaces, and interactions of biological macromolecules.
How to open CUBE file?
CUBE file can be opened and referenced using the following programs.
- NWChem (Free) for (Windows, MAC, Linux)
