Free chemistry software for linux

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. Jmol is cross-platform, running on Linux/Unix, Mac OS X, and Windows systems.
- The JmolApplet is a web browser applet that can be integrated into web pages.
- The Jmol application is a standalone Java application that runs on the desktop.
- The JmolViewer is a development tool kit that can be integrated into other Java applications.
Main features:
- Free, open-source software licensed under the GNU Lesser General Public License
- Applet, Application, and Systems Integration Component
- Cross-platform
- Supports all major web browsers
- High-performance 3D rendering with no hardware requirements
- File formats
- Animations
- Vibrations
- basic unit-cell support
- schematic shapes for secondary structures
- measurements
- RasMol/Chime scripting language support
- JavaScript support library
- Exports to .jpg, .pdf, and PovRay
Jmol v10 is a complete rearchitecture and rewrite of Jmol, undertaken in the Spring of 2003, with the specific goal of developing Jmol into a replacement for the Chime Plug-in.
Jmol v10 retains most of the features and functionality of the previous Jmol releases while offering significant enhancments in the following areas:
- true 3D graphics engine that requires no special hardware
- 24 bit color with accurate lighting and shading
- substantially higher rendering performance
- handles large macromolecules with excellent performance
- protein/nucleic acid secondary structure graphics
- RasMol/Chime script compatibility
Enhancements:
- bug fix: isosurface color -- not operating for some isosurface types
- bug fix: isosurface "xxxx.cube" -- not assigning proper default colors
- bug fix: gamess reader MO fix
- bug fix: state save of STRUCTURE misplaced

LON-CAPA is an Open Source Freeware Distributed Learning Content Management and Assessment System.
LON-CAPA is a full-featured, web-based course management system similar to commercial systems, see edutools.info for comparisons.
Main features:
- Content sharing and content reusability, including
- Network of shared resources from 27 participating institutions
- Shared repository of 61,000 resources including assessment questions and multimedia content
- Easy semester transition
- A large set of resources in physics/astronomy, chemistry, biology, mathematics/statistics, and geology
- Ability to add new resources to the existing content pool
- Creation and grading of randomized homework, quizzes or exams, including the ability to
- create sophisticated question types such as: click-on image, random label, random plot, or formula response
- reduce blind copying of answers by giving a different version of the problems to each student
- print randomized bubblesheet exams and quizzes
- configure the reporting of grades and feedback with a wide variety of options
- contextualize threaded homework discussions
- A development group based that sustains a twice-yearly LON-CAPA release cycle to insure rapid incorporation of instructor-requested enhancements.
- An open-source freeware system
Whats New in 2.4.2 Stable Release:
- This release correctly installs the jsMath fonts, which are used for TeX rendering.
- Symbolic math input now gets correctly compared to the instructor-prepared sample answer.
- Several issues regarding the printing, rendering, and grading of ".page" content assemblies were resolved.
- Teaching Assistants can now grade assignments that have an encrypted URL.
- The character "@" is now allowed in usernames.
- The German localization file was updated.
- Installation on CentOS and Scientific Linux is now possible.
Whats New in 2.4.99.0 Development Release:
- This release candidate supports personal response system ("clicker") registration and uploading of associated session data.
- It also offers new search functionality for users in and outside of classes, as well as optional coupling to institutional directories. User menu buttons can be switched off.
- Dynamics graphing in homework problems now supports linear/log, log/linear, and log/log plots.

GChemPaint is a 2D chemical structures editor for the Gnome desktop.

GChemPaint should enable embedding some chemistry in files from other programs using Bonobo.

Units-filter is a basic standalone filter written in C, flex, and bison.
It inputs strings like "1.5e3 nN.m.s^-1" (which could be the time growth ratio of a torque) and outputs the value in standard SI units, followed by the physical dimension of this value.
units-filter can be embedded in educational test systems, in order to analyze a students answer to a problem of physics or chemistry.
Enhancements:
- The support for quantities with a particular number of significative digits was added.
- For example, the entry "1.02m#5" or "1.0200m" are equivalent and signify a distance measurement precise at the sub-millimeter scale.
- Both would yield the output "1.0200e+00 m".

XMDS project is a code generator that integrates equations. You write them down in human readable form in an XML file, and it goes away and writes and compiles a C++ program that integrates those equations as fast as it can possibly be done in your architecture.
xmds - the eXtensible Multi-Dimensional Simulator - is a program for solving equations - fast. It is a tool to simplify the computer modelling of various systems, and is currently being developed within the Australian Centre for Quantum-Atom Optics at the University of Queensland.
There are many situations in many areas where a system of interest can be modelled by a differential equation or equations. Such areas include: physics, mathematics, engineering, physical and theoretical chemistry, theoretical and computational biology, finance, and economics. Modelling these systems involves writing a computer program to find a solution to the equations, which is not necessarily easy to do.
This is where xmds comes in. The advantage of using xmds instead of doing the same job by means of conventional programming is the same as ordering a pizza as opposed to making one yourself. The only thing you have to learn to become an xmds user is "How to order a pizza".
There are a couple of important differences here though: normally you have to pay for the pizza, while xmds comes for free; and xmds is like a gourmet pizza outlet - one has the option of exotic things like solving stochastic equations, which the chain-brand "pizza vendors" dont offer! xmds therefore makes writing complex computer simulations simple.
Another major advantage of xmds is that it is free. The source code and documentation can be freely downloaded from the xmds web site. xmds runs on Linux, Unix (including MacOS X) and the Cygwin environment on Windows, help for installing xmds on these systems is available both from the web site and the xmds distribution.
xmds is especially useful in solving complex problems requiring solving the problem over many different random parameters. Such problems can be parallelised (run on lots of computers at the same time) and xmds does this automatically with little user input, making the solution of these problems a breeze.
Often writing a computer program to solve complex problems can be very difficult, time-consuming, and error-prone. This is where xmds excels. One merely needs to write a script in a high-level form which is easy for a person to understand, and xmds goes off and writes the low-level code for you, producing code that is better for a computer.
This makes the writing of a simulation program significantly easier, reducing the development time, and almost eliminating bugs since xmds has written the vast majority of the code for you and has used thoroughly tested code and techniques in the production of the program.
The output program that xmds writes is still about as fast as code hand-written by an expert, so one can has the best of both worlds: quick development time, and quick execution.
So, if youre trying to model a bunch of atoms bouncing around together, the diffusion of an electrolyte solution, the reaction of enzymes with a substrate, or the volatility of stock prices, then xmds is the simulation tool for you.
Main features:
- An open-source XML based simulation package
- From Ordinary Differential Equations (ODEs) up to stochastic Partial Differential Equations (PDEs)
- Many applications:
- physics
- mathematics
- engineering
- finance
- economics
- chemistry
- theoretical biology
- Generates fast, C++ compiled code
- Documentation and source are free!
- Runs on Linux, Unix, MacOS X and Cygwin (Windows)
Installation
tar -xzvf xmds-1.3-5.tar.gz
cd xmds-1.3-5
./configure --with-user (or if logged on as root ./configure)
make
make install
Enhancements:
- This is another bugfix release of xmds-1.6.
- It is unlikely that anyone else has ever encountered these bugs, and now they never will. We are back to "no known bugs".

KryoMol project is a KDE based program for visualization and analysis of several chemistry related files. Currently KryoMol can cope with:
- Quantum Chemical Computation logs from Gaussian98/03, GAMESS, ACESII (german version), and NwChem
- Molecular Mechanis Logs: Tinker, Macromodel
- Other formats as xyz or mol
- 1D NMR spectra and JCAMP-DX spectra
Installation:
KryoMol is a autoconf/automake based program and installs itself with the common configure/make/make install procedure.
Installation as root
$ ./configure
$ make
$su
$make install
and now log out and log in ( I strongly recommend this to properly load all new libraries and services).
Installation as user
If you dont have root privileges and want to try KryoMol you must install it in a directory with write permissions, therefore you must use the prefix switch in configure. For instance if you want to install under your personal kde tree $./configure --prefix=/home/user/.kde
$make
$make install
log out and log in
Installation as user in a new kde tree
If you want to install in a compleptly new KDE tree, for instance /home/user/mykde you must follow the above procedure:
$./configure --prefix=/home/armando/mykde && make && make install
and now add this to your .bash_profile:
MYKDE=/home/armando/mykde
export KDEDIRS=$MYKDE:$KDEDIRS
export LD_LIBRARY_PATH=$MYKDE/lib64:$LD_LIBRARY_PATH
export PATH=$MYKDE/bin:$PATH
Enhancements:
- ECD/VCD/UV spectra are properly represented
- Scale is draw in UV/ECD spectra
- Solved problem with capitalized extensions
- Solved problems in xyz parser
- Solved problem when closing window and animation is active
- Solved a bug in the varian nmr parser
- Opening of nmr spectra over remote protocols
- Solved bug in format when exporting hessian
- Replaced some old QFileDialog and QPrinter stuff by KDE widgets
- Solved problem when loading printer icon on QIRWidget

Parallel Three-Dimensional Fast Fourier Transforms, dubbed P3DFFT, is a library for computational computing in a wide range of sciences, such as physics, climatology, chemistry.
This project was developed at SDSC by Dmitry Pekurovsky as a product of a Strategic Applications Collaborations (SAC) project.
Main features:
- Parallel implementation with 2D data decomposition, overcoming an important limitation to scalability of other 3D FFT libraries implementing 1D, or slab, decomposition.
- Optimized for parallel communication and single-CPU performance.
- Built on top of well-optimized and flexible 1D FFT libraries.
Enhancements:
- Assorted minor bugfixes and code speedups.

VULCAN project provides computational fluid dynamics analysis.
VULCAN (Viscous Upwind aLgorithm for Complex flow ANalysis) offers computational fluid dynamics for subsonic speed through hypersonic turbulent reacting and non-reacting flows on a variety of serial and parallel computational platforms.
The computational cost of propulsion flow analysis is reduced through the use of special turbulent wall treatments, multi-grid methods for elliptic and space marching schemes, and conditioning of the governing equations to reduce numerical stiffness.
Physical modeling capabilities are improved through the inclusion of models for compressibility, Reynolds stress anisotropies, turbulent diffusivity, finite rate chemistry, and turbulence/chemistry interaction effects.
VULCAN can simulate two-dimensional, three-dimensional, or axi-symmetric multi-block problems.
Enhancements:
- This release adds logic to force the correct asymptotic behavior of the turbulence kinetic energy and the turbulence frequency (omega) for surface cell y+ values that are below the log layer portion of the boundary layer.
- It adds the output of reference stagnation conditions and dynamic pressure.
- There are numerous bugfixes, code cleanups, and fixes for setting initial conditions.
- There are minor GUI enhancements.