Software Packages and Libraries
Molecular modeling and simulation softwares
  • NAMD : Scalable Molecular Dynamics 
  • CHARMM  : Chemistry at HARvard Macromolecular Mechanics
  • LAMMPS :  Molecular dynamics simulator
  • CHARMM-GUI :  Effective charmm input generator
  • Gromacs :  Molecular dynamics engine
  • VMD : Visual  Molecular Dynamics
  • Pymol : Molecular viewer
  • AUTODOCK : a suite of automated docking tools
  • APBS : a software for evaluating the electrostatic properties of biomolecular systems
  • SIMTK.org :  open access to simulations tools, accurate models and the people behind them
  • SDF toolkit : provide functions to read and parse SDFs, filter and add/remove properties
  • OpenBabel :  a chemical toolbox that is designed to speak the many languages of chemical data
  • TINKER :  software tools for molecular design
  • WHATIF :  molecular modeling package

Graphing and visualization
  • GNUPLOT : a portable command-line driven graphing utility
  • Xmgrace :  plotting tool for the X-window system
  • OpenDX :  make your data come to life

 Numerical libraries, platforms and codes
  • Netlib : Optimized linear algebra libraries such as BLAS and LAPACK
  • GAMS :  guide to available mathematical software
  • MINPACK :  portable library for solving nonlinear systems of equations and nonlinear least square
  • ADIFOR :  automatic differentiation of fortran
  • Octave :  high-level language intended for numerical compuations
  • AUTO :   Software for continuation and bifurication problems in ordinary differential equations

Other useful software
  • JabRef : open source bibliography  reference manager
  • Engauge Digitizer :  converts and image file showing a graph or map into numbers
©  Abdallah Sayyed-Ahmad 2010