"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
Gaussian 09 is designed to model a broad range of molecular systems under a variety of conditions, it performs its computations starting from the basic laws of quantum mechanics.
MATLAB integrates mathematical computing, visualization, and a powerful language to provide a flexible environment for technical computing. The open architecture makes it easy to use MATLAB and its companion products to explore data, create algorithms, and create custom tools that provide early insights and competitive advantages. Documentation on Matlab is available here.
From simple calculator operations to large-scale programming and interactive document preparation, Mathematica is the tool of choice at the frontiers of scientific research, in engineering analysis and modeling.
Intel Composer XE 2011
Software Development Environment/Tools. Optimized C, C++, and Fortran compilers, scalable multithreading with OpenMP, new parallelism models, and Co-Array Fortran as part of the Fortran 2008 standard, including optimized libraries. A simple recompile with Intel Composer XE compilers can boost performance by 20 percent or more.
Documentation and Manuals
There is a wide range of software available at CCS. Here are various links to documentation to much of this software and general UNIX questions.
Free Software Foundation GNU Make.
GNU Make manual in various formats.
Free Software Foundation GNU Emacs.
GNU Emacs manual in various formats.
Free Software Foundation GNU GCC.
GNU GCC 4.3.1 manual.
Free Software Foundation GNU Plotutils.
GNU Plotutils manual in various formats.