LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It’s written in C++ and is open source.
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Category: Scientific
tomviz – processing, visualization, and analysis of 3D tomographic data
The Tomviz project is a cross platform, open source application for the processing, visualization, and analysis of 3D tomographic data.
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GROMACS – versatile package to perform molecular dynamics
GROMACS is a molecular dynamics simulator, with building and analysis tools. It’s a versatile package to perform molecular dynamics.
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Psi4 – quantum chemistry software package
Psi4 is a suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations.
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GAMESS – ab initio molecular electronic structure software
The General Atomic and Molecular Electronic Structure System (GAMESS) is a free and open source general ab initio quantum chemistry package.
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MPQC – Massively Parallel Quantum Chemistry software
MPQC (Massively Parallel Quantum Chemistry Program) is software that computes properties of atoms and molecules from first principles.
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NWChem – chemistry software
NWChem is an ab initio computational chemistry software package that is suitable to perform complex calculations on molecular structure.
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Avogadro – advanced molecule editor and visualizer
Avogadro is an advanced open source molecular editor designed for cross-platform use in computational chemistry, and other areas.
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PyMOL – molecular visualization system software
PyMOL is a molecular graphics system designed for real-time visualization and molecular graphics images and animations.
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CP2K – atomistic simulations of solid state, liquid, molecular and biological systems
CP2K is a free and open source quantum chemistry and solid state physics software package that can perform atomistic simulations.
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Open Babel – chemical toolbox software
Open Babel is a version of the Babel chemistry file translation program. Convert, analyze, or store data from molecular modeling.
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Gabedit – GUI to computational chemistry packages
Gabedit is a graphical user interface to Gamess-US, Gaussian, Molcas, Molpro, MPQC, PCGamess and Q-Chem computational chemistry packages.
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Jmol – viewer for chemical structures in 3D
Jmol is a Java viewer for three-dimensional chemical structures with features for chemicals, crystals, materials and biomolecules.
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Kalzium – periodic system of the elements
Kalzium is a chemistry application for KDE 5, including a Periodic Table of Elements, chemical reference, chemical equation solver, and more.
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XDrawChem – molecule structure drawing
XDrawChem is a 2D editor for chemical structures and reactions. It mirrors the abilities of the commercial ChemDraw suite.
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MoleQueue – abstract, manage, and coordinate the execution of tasks
MoleQueue is a C++ desktop application for abstracting, managing, and coordinating the execution of tasks.
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BKChem – chemical drawing program
BKChem is a free and open source 2D molecule editor written in Python. It has a wealth of features but is simple to use.
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MITIE: MIT Information Extraction
MITIE: MIT Information Extraction offers state-of-the-art information extraction tools. MITIE is free and open source software.
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text2vec – R package – framework with API for text analysis and natural language processing
text2vec is an R package which provides an efficient framework with a concise API for text analysis and natural language processing (NLP).
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Moses – statistical machine translation system
Moses is a statistical machine translation system to automatically train translation models for any language pair.
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