Molecular Sciences – Software / Apps

Chemistry is at the heart of molecular sciences and involves the study of matter and thebiochem_BallStick_Logo1 changes it undergoes. Chemistry deals with a molecular scale and atomic interpretation of the world we live in, helping us to understand that world. Chemistry is regarded as the central science, given its close links with physics and engineering, with biology and medicine, and with geology and earth science.

 At a fundamental level we are all chemists

(or molecular scientists)

Each time we breathe, boil water, start a fire, a chemical reaction takes place. We develop and function as a consequence of chemical processes taking place in our body. Chemistry therefore plays a significant role in everyone’s lives.atomic33

This blog post focuses on selecting the best open source software for chemistry and the general field of molecular science. Hopefully there will be something for interest here for all budding chemists.

VMD Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
Tomviz Process, visualize, and analyze 3D tomographic data
GROMACS Versatile package to perform molecular dynamics
Psi4 Ab initio quantum chemistry software
GAMESS General ab initio quantum chemistry package
MPQC Computes the properties of molecules, ab initio
NWChem Ab initio computational chemistry software package
Avogadro Advanced molecular editor
PyMOL OpenGL molecular graphics system written in Python
CP2K Atomistic simulations of solid state, liquid, molecular and biological systems
Open Babel Converts and manipulates chemical data files
Gabedit Graphical user interface to computational chemistry packages
Jmol Viewer for three-dimensional chemical structures
Kalzium Full-featured chemistry application for KDE 5 (Linux) – Periodic Table
XDrawChem 2D editor for chemical structures and reactions
MoleQueue Abstract, manage, and coordinate the execution of tasks
BKChem 2D molecule editor written in Python
Chemissian Analysis tool of molecules electronic structure and spectra.
ORCA (Alt) General-purpose quantum chemistry program package.
NAMD Molecular dynamics code designed for high-performance simulation of large biomolecular systems.
CHIMERA Program for interactive visualization and analysis of molecular structures.
Tinker Suite of Molecular modeling software tools
NMRdb NMR spectroscopy prediction tool.

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