Molecular Simulation Packages
AMBER – Assisted Model Building with Energy Refinement: A package of molecular simulation programs developed by several groups in the USA.
CHARMM – Chemistry at HARvard Macromolecular Mechanics: Another package to perform molecular dynamics developed by several groups in the USA.
NAMD – A parallel MD code designed for high-performance simulation of large biomolecular systems developed by Klaus Schulten’s group at UIUC.
GROMOS – GROningen MOlecular Simulation computer program package: Another package of molecular simulation programs developed in ETH, the Swiss Federal Institute of Technology, Zürich, Switzerland.
GROMACS – Another package to perform molecular dynamics developed by several Swedish groups.
ab initio Quantum Chemistry Packages
Gaussian – A connected system of programs for performing semi-empirical and ab initio molecular orbital (MO) quantum chemical calculations.
GAMESS – The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.
Q-CHEM – A comprehensive ab initio quantum chemistry package for accurate predictions of molecular structures.
NWCHEM – An ab initio computational chemistry software package, which also includes quantum chemical and molecular dynamics functionality. It is actively developed by a consortium of developers and maintained by the EMSL located at the Pacific Northwest National Laboratory (PNNL) in Washington State.
Other Useful Software
VMD – A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
OpenBabel – A chemical toolbox designed to search, convert, analyze, or store data from molecular modeling, chemistry, biochemistry, or related areas.
GRASP – A molecular visualization and analysis program, which is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties.
3DNA – A package for the analysis, rebuilding, and visualization of 3D nucleic acid structures.
SPARKY – A graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.
NMRPipe – A program for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis.
Delphi – A program that provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution.
GNUPlot – A free, command-driven, interactive, function and data plotting program.
GRACE – A 2D plotting tool for the X Window System.
JOE – My favorite text editor, which is capable of emulating WordStar, Pico, and Emacs.
© YildirimLab 2017 (updated 6/25/2024)
