AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock has been widely used and there are many examples of its successful application in the...
ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. ABINIT also includes...
ADF (Amsterdam Density Functional) is a complete computational chemistry suite with a fully integrated GUI for easy setup and analysis. At HPCVL, the following packages are available:
AMBER is a set of molecular mechanical force fields for the simulation of biomolecules; and a package of molecular simulation programs which includes source code and demos.
The CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio Molecular Dynamics simulation as described by Car and Parinello. CPMD runs on many different computer architectures and it is well parallelized.
The CRYSTAL package performs ab-initio calculations on the ground-state energy, electronic wave function and properties of periodic systems. Hartree-Fock and Kohn-Sham Hamiltonians (DFT) can be used. Systems may be periodic in 0 (molecules), 1 (polymers), 2 (slabs) or 3 dimensions (crystals)....
The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. It is particularly suitable for controlled limited or full CI calculations. GAMESS is able to utilize multiple processors. It is maintained by the members of the Gordon...
Gaussian is a computational chemistry package that has become the standard code for fast electronic structure calculations. It is able to utilize shared-memory multi-processor architectures. Gaussian has been developed over the course of several decades by a host of people, and is now...
NAMD is a parallel code for molecular dynamics simulation of large biomolecular systems, developed by the Theoretical Biophysics Group ("TBG") in the Beckman Institute of the University of Illinois.
NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources...
Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving, ultrasoft, and PAW). Quantum ESPRESSO builds onto newly-...
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. It is mainly used for linear-scaling ab-...
FFTW is allegedly the Fastest Fourier Transform in the West. The package was developed by Matteo Frigo and Steven G. Johnson at MIT and is free software. It consists of C-routines that are accessible via a library archive, and...
MATLAB® is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numeric computation. You can use MATLAB in a wide range of applications, including signal and image processing, communications, control design, test...
The NAG libraries and supporting software are a large collection of numerical routines ranging from simple implementations of special functions to complex optimization techniques. The libraries include:
ETSc, the Portable Extensible Toolkit for Scientific computation, is a suite of data structures and routines for the parallel (and serial) implementation of large scale application codes. PETSc uses the MPI library for its message-passing communications.
The ABAQUS suite of software for finite element analysis (FEA) consists of three core products - ABAQUS/Standard, ABAQUS/Explicit and ABAQUS/CAE. ABAQUS/Standard is used to solve traditional implicit finite element analyses, such as static, dynamics, thermal with a wide range of contact and...
Adina is a comprehensive finite-element system that may be used for structural analysis, simulation of fluids, and computations on the interaction of fluids with structures. It is designed with ease of use and broad applicapility in mind. It provides a grahical user interface and can be used on...
FIDAP is a finite-element based fluid dynamics analysis package. It allows the modeling of fluid flow, heat transfer and related phenomena in complex geometries. Problems can be solved on unstructure meshes that may be created with ease. The package consists of several modules which may be...
FLUENT is a state-of-the-art computer program for modeling fluid flow and heat transfer in complex geometries. It provides adaptive mesh capabilities and may be run in parallel. It is written in C and uses a client/server architecture. It provides a graphical user interface as well as a batch...
The OpenFOAM® (Open Field Operation and Manipulation) CFD Toolbox is a free, open source CFD software package produced by a commercial company, OpenCFD Ltd. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an...
The Iris Explorer is a very powerful visualization tool. It is designed in a modular manner to offer maximum flexibility and feartures an intuitive point-and click interface. Visualizations ranging from simple bar graphs to complex color-coded contour graphics on 3D objects are...