Scientific Software

Several scientific software packages are installed on the HPCC, which allows the Siena community to solve computational problems from many different fields: molecular dynamics simulations, biochemical systems, electronic structure calculations, mathematics, visualization, computer science, and general utilities.

Molecular Dynamics Simulations

CHARMM- (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems.

http://www.charmm.org/documentation/overview.html

Amber12- "Assisted Model Building with Energy Refinement" A suite of around 50 programs designed to facilitate molecular dynamics simulation of large-scale systems.

http://ambermd.org/#Amber12

Gromacs-A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software.

http://www.gromacs.org/

LAMMPS-a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator

http://lammps.sandia.gov/

Biochemical Systems

ViennaRNA- a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

http://www.tbi.univie.ac.at/RNA/

BLAST-The Basic Local Alignment Search Tool finds regions of local similarity between sequences.

http://blast.ncbi.nlm.nih.gov/Blast.cgi

Mfold- a program to obtain suboptimal structures, which provide significant information.

http://mfold.rna.albany.edu/?q=mfold

Electronic Structure Calculations

Gamess-An ab initio quantum chemistry package.

http://www.msg.ameslab.gov/gamess/documentation.html

Firefly8-An ab initio quantum chemistry package.

http://classic.chem.msu.su/gran/gamess/

Gaussian09-An ab initio quantum chemistry package.

http://www.gaussian.com/g_tech/g_ur/g09help.htm

NWChem-An ab initio quantum chemistry package.

http://www.nwchem-sw.org/index.php/Main_Page

Mopac2012 semi-empirical quantum chemistry package.

http://openmopac.net/manual/

Mathematics

Octave-a high-level interpreted language, primarily intended for numerical computations.

http://www.gnu.org/software/octave/

Scilab-is an open source, cross-platform numerical computational package and a high-level, numerically oriented programming language.

http://www.scilab.org/

Visualization

IDL-short for Interactive Data Language, is a programming language used for data analysis. It is popular in particular areas of science, such as astronomy and medical imaging.

http://www.exelisvis.com/docs/using_idl_home.html

Povray-Persistence of Vision Raytracer, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms.

http://www.povray.org/

Bioblender-BioBlender is a software package built on the open-source 3D modeling software Blender. Biology works at nanoscale, with objects invisible to the human eye. With BioBlender it is possible to show some of the characters that populate our cells, based on scientific data and the highest standard of 3D manipulation.

http://bioblender.eu/

Blender-is a free and open-source 3D computer graphics software product used for creating animated films, visual effects, art, 3D printed models, and interactive 3D applications.

http://www.blender.org/

NBO6- Natural Bonding Orbital 6 is a program that interfaces with electronic structure software and produces output ideal for visualization of the results.

http://nbo6.chem.wisc.edu/nboman.pdf

Computer Science

MySQL Cluster-is designed to provide high availability and high throughput with low latency, while allowing for near linear scalability.

http://www.mysql.com/products/cluster/

Java JDK-Java development kit.

http://www.oracle.com/technetwork/java/javase/downloads/index.html

General Utilities

Intel Compiler Suite- Intel C, C++, and Fortran compiler along with the Intel Math Kernel Library.

http://software.intel.com/en-us/intel-compilers

FFTW- The Fastest Fourier Transform in the West (FFTW) is a software library for computing discrete Fourier transforms (DFTs) developed by Matteo Frigo and Steven G. Johnson at the Massachusetts Institute of Technology. FFTW is known as the fastest free software implementation of the Fast Fourier transform (FFT) algorithm. It can compute transforms of real and complex-valued arrays of arbitrary size and dimension in O(n log n) time.

http://www.fftw.org/

HDF5- Hierarchical Data Format is the name of a set of file formats and libraries designed to store and organize large amounts of numerical data.

http://www.hdfgroup.org/HDF5/