Index of specialist software¶
Amber¶
Assisted Model Building with Energy Refinement (AMBER) is a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman’s group at the University of California, San Francisco.
sudo yum install amber16
autodock¶
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.
sudo yum install autodock426
Avogadro¶
Avogadro is an advanced molecule editor and visualizer designed for cross platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
sudo yum install avogadro120
BIOVIA Discovery Studio¶
Built on the BIOVIA Foundation, Discovery Studio is BIOVIA’s comprehensive predictive science application for the Life Sciences.
sudo yum install biovia-discovery-studio-2016
CCDC CSD System¶
For chemists in academia and industry wanting to discover, access and visualise crystal structures easily to support their research. The CSD-System brings you the essential crystallographic and structural chemistry capabilities to deliver knowledge from the CSD.
sudo yum install ccdc2017
DL_POLY¶
DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.
sudo yum install dlpoly408
Dropbox¶
Dropbox is the gold standard file hosting and synchronisation solution for modern operating systems. Although we provide this package we offer no support for Dropbox and please do not store any university data within your Dropbox account.
sudo yum install nautilus-dropbox
FFTW¶
FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT) in one or more dimensions, of both real and complex data, and of arbitrary input size.
sudo yum install fftw fftw-devel
GNU Plot¶
Gnuplot is a command-line driven, interactive function plotting program especially suited for scientific data representation. Gnuplot can be used to plot functions and data points in both two and three dimensions and in many different formats.
sudo yum install gnuplot501
GROMACS¶
GROMACS is a versatile package to perform molecular dynamics.
- 4.6.7:
sudo yum install gromacs467 - 5.1.4:
sudo yum install gromacs514
GSView¶
A user friendly viewer for Postscript, PDF, XPS, EPUB1, CBZ, JPEG and PNG files.
sudo yum install gsview60
LAMMPS¶
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
sudo yum install lammps lammps-doc lammps-openmpi lammps-python
latexmk¶
A make-like utility for LaTeX files. Latexmk is a Perl script for running LaTeX the correct number of times to resolve cross references, etc.
sudo yum install latexmk
libxc¶
Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by all the ETSF codes and also other codes.
sudo yum install libxc300
lyx¶
LyX is a WYSIYM (What You See Is What You Mean) document editor that acts as a front-end for TeX/LaTeX.
sudo yum install lyx
Marvin Suite¶
Marvin Suite is a series of applications and an API for chemical sketching, visualisation and data exploration.
sudo yum install Marvin
Mathematica¶
Wolfram Mathematica is a mathematical symbolic computation program, sometimes termed a computer algebra system or program, used in many scientific, engineering, mathematical, and computing fields.
sudo yum install mathematica1101
MatLab¶
MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment and fourth-generation programming language.
sudo yum install matlab2016b
Mendeley Desktop¶
Mendeley Desktop lets you save PDFs, share thoughts with colleagues and automatically back up and sync your files across different computers.
sudo yum install mendeley1178
Mercury¶
Crystal Structure Visualisation, Exploration and Analysis Made Easy. Mercury offers a comprehensive range of tools for 3D structure visualization and the exploration of crystal packing.
sudo yum install mercury39
MOE¶
Molecular Operating Environment (MOE) is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package.
sudo yum install moe20160802
netcdf¶
A set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
sudo yum install netcdf
NWChem¶
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
sudo yum install nwchem nwchem-openmpi
Octave¶
GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.
sudo yum install octave420
Povray¶
The Persistence of Vision Ray Tracer, or PoV-Ray is a ray-tracing program which generates images from a text-based description of a scene.
sudo yum install povray37
PyMol¶
PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies.
sudo yum install pymol1840
R, RStudio and RStudio Server¶
See R
RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, and workspace management.
sudo yum install rstudiosudo yum install rstudio-server
SageMath¶
SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more.
sudo yum install sagemath751
Team Viewer¶
TeamViewer is a proprietary computer software package for remote control, desktop sharing, online meetings, web conferencing and file transfer between computers.
sudo yum install teamviewer
texlive¶
See TeX Live (LaTeX)
USCF Chimera¶
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
sudo yum install chimera1112
VirtualBox¶
VirtualBox is a powerful PC virtualization solution allowing you to run a wide range of PC operating systems on your Linux system. This includes Windows, Linux, FreeBSD, DOS, OpenBSD and others.
sudo yum install VirtualBox-5.1
VisIT¶
VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.
sudo yum install visit2121
VMD¶
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
sudo yum install vmd193
VTK¶
VTK is an open-source software system for image processing, 3D graphics, volume rendering and visualization. VTK includes many advanced algorithms (e.g., surface reconstruction, implicit modeling, decimation) and rendering techniques (e.g., hardware-accelerated volume rendering, LOD control).
sudo yum install vtk vtk-qt
xmgrace¶
Grace is a WYSIWYG 2D plotting tool for the X Window System and Motif.
sudo yum install xmgrace5125
xpdf¶
Xpdf is a legacy viewer for Portable Document Format (PDF) files. Xpdf is a small and efficient program which uses standard X fonts.
sudo yum install xpdf
Zim Desktop Wiki¶
Zim is a WYSIWYG text editor written in PyGTK which aims to bring the concept of a wiki to your desktop. Every page is saved as a text file with wiki markup. Pages can contain links to other pages, and are saved automatically.
sudo yum install zim
Zotero¶
Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share your research sources.
sudo yum install zotero402910