In the preceding sections we described numerical libraries, that is, software that can be linked to application programs that you write. In this section we list some stand-alone scientific applications that can run on Linux clusters. Such applications typically take an input file of model parameters and specifications and output another file containing the results of the calculation. The following list is obviously incomplete: for each application area there are several applications with similar functionality, and more applications are released all the time.
Gaussian  is a connected system of programs for performing semi-empirical and ab initio molecular orbital quantum chemical calculations. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds that are difficult or impossible to observe experimentally, such as short-lived intermediates and transition structures. It is currently available for Unix/Linux, MS Windows, and Mac OS X platforms.
Fluent  is a computational fluid dynamics package, used for such applications as environmental control systems, rotor-airframe interactions, propulsion, reactor modeling, airflow around buildings, rotating cavities, fan noise modeling, and vortex shedding. It is available for Unix/Linux and MS Windows clusters.
MSC/Nastran  is a computer aided engineering / structural finite element application developed by NASA. It is available for Unix/Linux platforms, MS Windows, and vector machines such as Fujitsu and NEC.
LS-DYNA  is a general-purpose transient dynamic finite element program. LS-DYNA is optimized for shared- and distributed-memory Unix, Linux, and Windows-based platforms. LS-DYNA Applications include crashworthiness, occupant safety, metal forming, biomedical, fluid-structure interaction, and earthquake engineering.
NAMD  is a molecular dynamics code, available for workstation clusters with Unix/Linux, MS Windows, or Mac OS X.
NWChem  provides many methods to compute the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. In addition, NWChem can perform classical molecular dynamics and free energy simulations. It is available free of charge (certain countries embargoed), with support for various Unix/Linux clusters, MS Windows, and vector computers such as the Fujitsu VPP.