Atoms Molecules Ions

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded... Platforms: Mac, Linux

This highly functional and easy to use Scientific Calculator is a must for science students. The main calculator has over 40 functions while an extensive number of utilities, tools and science data reference systems can be called. The calculator contains one of the most extensive measurement... Platforms: Windows, Windows 8, Windows 7, Windows Server

MOPlot is a handy visualization application specially designed for fast molecular orbitals plotting from the outputs of the Gaussian 03/98/94, Molcas, Gamess/US quantum chemical calculation packages. This Molecular Orbital Plotting Program will prove to be easy-to-use and very efficient. MOPlot... Platforms: Windows, XP

MRMer reads an mzXML file and infers precursor-ion/product-ion relationships. It displays elution curves of the product ions and allows the user to select or deselect them as candidates for MRM-based assays. MRMer also displays the elution curve of the precursor ions when MS1 scans are present... Platforms: Windows

SketchEl is an interactive chemical molecule sketching tool, and molecular spreadsheet data entry application. The feature set provided by the molecular sketcher is largely limited to the minimum features required to conveniently edit diagram representations of small molecule structures.... Platforms: Windows

States of Matter: Basics is a simple and easy-to-use Java simulation that has been designed to allow you to watch different types of molecules form a solid, liquid, or gas. Change the temperature or volume of a container and see a pressure-temperature diagram respond in real time. Relate the... Platforms: Windows, Windows Vista, 7

The Ascalaph Quantum package provides interfaces to ab initio quantum mechanical packages NWChem, CP2K and PC GAMESS / Firefly. Quantum calculations are performed using the PC GAMESS program. FEATURES: Energy calculations : · Energy calculation mode is controlled by selecting the basis... Platforms: Windows

PyMOL is a user-sponsored molecular visualization system on an open-source foundation. Please support development of this open, effective, and affordable software by purchasing an incentive copy, which is pre-built and comes with maintenance and support. PyMOL can interpret over 30 different... Platforms: Windows, Mac, Linux

APBSmem is a handy, Java-based graphical user interface specially designed to help you with Poisson-Boltzmann electrostatics calculations at the membrane. The Poisson-Boltzmann equation or PB describes the electrostatic environment of a solute in a solvent containing ions. Platforms: Windows

Molecules and Light is a Java application designed to enable you to observe the interaction of light and molecules. Do you ever wonder how a greenhouse gas affects the climate, or why the ozone layer is important? Now you can find out, with the aid of this application. for WindowsAll Platforms: Windows

APBS was designed as a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation or PBE. PBE is one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum... Platforms: Windows

123Tag is an easy-to-use and powerful Tag editor and file renamer for MP3,MP4,WMA and many other audio formats, useful to manage and catalog all your music files. 123Tag helps you also to find and catalog  the huge amount of music files that usually are stored and disperded on your PC,... Platforms: Windows, Windows 7, Windows Server, Other

For the set of chemical elements (Ba, Sr, Ca and so on) there is a function enabling to print capital and small letters without switching by "Shift" and "Caps Lock" keys. Figures specifying the number of atoms in chemical formula (H2SO4) are automatically made subscripts, and atom's oxidation... Platforms: Windows

Suite of freeware tools for automating work of rendering and animating molecules Platforms: Windows

LAMMPS project is a Molecular Dynamics Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grain systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the mesoscale... Platforms: *nix

Chemistry::Mol is a molecule object toolkit. SYNOPSIS use Chemistry::Mol; $mol = Chemistry::Mol->new(id => "mol_id", name => "my molecule"); $c = $mol->new_atom(symbol => "C", coords => [0,0,0]); $o = $mol->new_atom(symbol => "O", coords => [0,0,1.23]); $mol->new_bond(atoms => [$c, $o],... Platforms: *nix

vID Infiltr8 is an opensourced metadata tagger for MPEG-4 files. The opensourced command line program AtomicParsley is wrapped in a familiar GUI to set persistent metadata into files. Multiple pieces of artwork & a subset of video-related tags are supported. Batch editing is fully supported and... Platforms: Mac

FieldLines is a screen saver that simulates the electric field lines emitted by charged particles. In this screen saver, ions move around the screen and bind to the lines of other ions as they get close and unbind as they move away. As the original author has said, physics never looked so good.... Platforms: Mac

LMarbles is an Atomix clone with a slight change in concept. Instead of assembling molecules you create figures out of marbles. Nevertheless, the basic game play is the same: If a marble starts to move it will not stop until it hits a wall or another marble. To make it more interesting there... Platforms: *nix

Language::Basic::Expression is a Perl package to handle string, numeric, and boolean expressions. SYNOPSIS See Language::Basic for the overview of how the Language::Basic module works. This pod page is more technical. # Given an LB::Token::Group, create an expression I parse it my $exp =... Platforms: *nix