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Top : Software : Scientific : Chemistry : Computational

Highlights
5 best open source board games to play online
Board games have seen a resurgence in recent years, and Linux has a good range of board games to choose from. There is a credible implementation of Catan called Pioneers. But for my favourite implementations of classic board games to play online, check out the recommendations below.

(Read more)
Konqueror/Embedded
attempts to build up a special version of the web browsing component of the KDE browser Konqueror (in particular its html rendering engine khtml and its io subsystem)

Links:

  • BIGMAC
    BIGMAC is a general-purpose parallel CBMC code. Configurational Bias Monte Carlo (CBMC) is a recent technique to compute thermodynamic properties of flexible molecules.
  • BOSS
    (commercial) performs (a) Monte Carlo (MC) statistical mechanics simulations for solutes in a periodic solvent box, in a solvent cluster, or in a dielectric continuum including the gas phase, and (b) standard energy minimizations, normal mode analysis, and conformational searching
  • CAMEO
    (commercial) Computer Assisted Mechanistic Evaluation of Organic reactions (CAMEO) is an expert system that predicts the outcome of organic reactions given starting materials, reagents and reaction conditions.
  • ccwatcher
    ccwatcher monitors the progress of computational chemistry calculations during their runtime. It parses important output and plots SCF energies. ccwatcher is highly platform-independent thanks to Python and the Qt Toolkit.
  • ChemApp
    ChemApp provides the powerful calculation capabilities of ChemSage in the form of a programmer's library. It consists of a rich set of subroutines which provides all the necessary tools for the calculation of complex multicomponent, multiphase chemical equilibria and the determination of the associated energy balances.
  • ChemCalc
    ChemCalc is a calculator that is more oriented towards chemistry. Although starting out as a console app, it is a hope that an X11 interface will be designed at a later time.
  • CP-Optimizer
    CP-Optimizer is an automatic procedure to perform geometry optimisation and harmonic frequency calculations using GAUSSIAN package.
  • Dirac
    DIRAC is a FORTRAN (and a bit of C) code for relativistic molecular calculations based on the Dirac-Coulomb Hamiltonian. It has support for uncontracted and contracted basis sets.
  • DOCK
    DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known.
  • DYNAMO
    DYNAMO is a structure calculation and analysis system built as an extension of our TCL/TK interpreter NMRWish, so that analysis schemes and annealing protocols are TCL scripts, and therefore relatively short, easy, and flexible.
  • EChem++
    EChem++ is a software system based on an object oriented approach to electrochemical experimentation, simulation, and data analysis. Currently, development emphasis lies on the modelling and simulation as well as the analysis modules.
  • FlexS
    FlexS is a computer program for predicting ligand superpositions. For a given pair of ligands, FlexS predicts the conformation and orientation of one of the ligands relative to the other one. In FlexS the reference-ligand is assumed to be rigid, thus, it should be given in a conformation which is similar to the bound state.
  • FlexX
    FlexX is an extremely fast, robust, and highly configurable (FlexX-able) computer program for predicting protein-ligand interactions.
  • frowns
    Frowns is a chemoinformatics toolkit geared toward rapid development of chemistry related algorithms. It is written in almost 100% Python with a small portion written in C++. Frowns is loosely based on the PyDaylight API that Andrew Dalke wrote to wrap the daylight C API. In some cases programs written using PyDaylight will also work under Frowns with a few minor changes.
  • Gabedit
    Gabedit is a graphical interface to Molpro and Gaussian computational chemistry packages running locally or on a remote server. It includes a 3D molecule editor and viewer. Read more
  • GaussSum
    GaussSum is a collection of scripts which parse the output of Gaussian 03, Gaussian 98 or GAMESS calculation to extract useful information. This includes the progress of the SCF cycles, geometry optimisation, UV-Vis/IR/Raman spectra, MO levels, MO contributions and more.
  • GenChemLab
    GenChemLab is an OpenGL-based application intended to simulate several common general chemistry exercises. It is meant to be used to help students prepare for actual lab experience. It could also be used in cases where laboratory facilites are not accessible, for instance in K-12 schools or home schooling. Supported experiments include titration, calorimetry, freezing point depression, vapor pressure, and spectrophotometry.
  • Ghemical
    Ghemical is a computational chemistry software package released under the GNU GPL. It has a graphical user interface (which is based on GTK2), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models (there is an experimental Tripos 5.2-like force field for organic molecules). Also a tool for reduced protein models is included.
  • Ghemical-GMS
    The Ghemical-GMS project has implemented a set of features/additions to the Ghemical codebase which provide the ability to generate GAMESS input files and submit these files to a graphical GAMESS queue system (GTK-Gamess).
  • Isotopic Pattern Calculator
    IPC is a program that calculates the isotopic distribution of a given chemical formula. It gives the rel. intensities and the propability of the masses belonging to a molecule ion, fragment or whatever is represented by the given chemical formula. Furthernmore it can use GNUPlot to visualize the result.
  • Kemistry
    Kemistry is a collection of chemistry-related applications written for the KDE Desktop Environment. It includes KMolCalc, a molecular weight and elemental composition calculator, and KemBabel, a file conversion program based on Open Babel.
  • KMovisto
    KMovisto allows you to open GAUSSIAN files directly without conversions and you see the results of your optimizations.
  • MCCCS Towhee
    Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling.
  • MCPRO
    MCPRO performs Monte Carlo statistical mechanics simulations of peptides, proteins, and nucleic acids in solution; it was derived from BOSS, but makes extensive use of the concept of residues. Version 1.68 does not include conformational search, quantum mechanics, or normal mode calculations. The MC simulations can be performed in a periodic solvent box, in a solvent cluster, or in a dielectric continuum including the gas phase.
  • MetaSite
    MetaSite is a computational procedure specially designed to predict the site of metabolism for xenobiotics starting from the 3D structure of a compound. The site of metabolism can be described by a probability function Psm that is correlated to, and can be considered, the free energy of the Cyp-substrate recognition and reactivity process.
  • Molaris
    Molaris includes Enzymix: a macromolecular simulation program designed to study the functions of proteins ranging from ligand binding to free energy profiles of enzymatic reactions using the Empirical Valence Bond (EVB) approach and the Free Energy Perturbation (FEP) method and Polaris: a fast converging computational software based on the Protein Dipoles-Langevin Dipoles (PDLD) approach.
  • Open Babel
    Open Babel is a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry. Read more
  • OpenThermo
    OpenThermo is a program package for statistical thermodynamics computations beyond rigid rotor harmonic oscillator approximation (RRHOA), with taking into account internal rotations and vibration anharmonicity.
  • ORAC
    ORAC is a program for running classical simulations of biomolecules. Simulations can be carried out in the NVE, NPT, NHP, and NVT thermodynamic ensembles. The integration of the equations of motion in any ensemble can be carried out with the r-RESPA multiple time step integrator and electrostatic interactions can be handled with the Smooth Particle Mesh Ewald method.
  • PhosphoFind
    PhosphoFind locates and quantifies phosphorylated peptides and proteins from a set of four MALDI mass spectra run in linear positive (Lin+), linear negative (Lin-), reflectron positive (Refl+), and reflectron negative (Refl-) modes.
  • PWscf
    Plane-Wave Self-Consistent Field: a set of programs for electronic structure calculations within Density-Functional Theory and Density-Functional Perturbation Theory, using a Plane-Wave basis set and pseudopotentials
  • QMForge
    QMForge is a program used to analyze the results of quantum chemistry (DFT) calculations. Gaussian 98/03/09, ADF, GAMESS (US), GAMESS (UK), PC-GAMESS, Jaguar, and ORCA files are supported.
  • SimSoup
    SimSoup is a graphical Artificial Chemistry simulator for Linux and Windows. The program enables a Chemistry to be defined in terms of Molecule Types and the possible Interactions between them. A simulation run involves setting up a number of Molecules of various Molecule Types in a Reactor, and then allowing Interactions to take place over a period of time. Interactions taking place in the Reactor are shown on a graphical display.
  • Sparkle/AM1
    Sparkle/AM1 is a computational chemistry model which exploits the lanthanide series characteristics to accurately predict geometries of the coordination polyhedra of complexes of ions of the rare earth metals. It is distributed as an external file for MOPAC 93r2, and as the default model for a modified version of the public domain MOPAC 6.
  • SPASM
    SPatial Arrangements of Side chains and Main chains
  • SPROUT
    (commercial) SPROUT is the sixth generation of the successful, mature de novo ligand design system. Through its use at various academic, government and industrial molecular modeling research centers, the software has proven to be successful for the generation of novel active ligand molecules.
  • Turbomole
    (commercial) Turbomole is for standard quantum chemical applications (HF, DFT, MP2). Unlike many other programs, the main focus in the development of Turbomole has not been to implement all new methods and functionals, but to provide a fast and stable code which is able to treat molecules of industrial relevance at reasonable time and memory requirements.
  • VOIDOO
    VOIDOO is for detection of cavities in macromolecular structures. It uses an algorithm that makes it possible to detect even certain types of cavities that are connected to "the outside world". Three different types of cavity can be handled by VOIDOO: Vanderwaals cavities (the complement of the molecular Vanderwaals surface), probe-accessible cavities (the cavity volume that can be occupied by the centres of probe atoms) and MS-like probe-occupied cavities (the volume that can be occupied by probe atoms, i.e. including their radii).
  • XMakemol
    XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.
  • XMolCalc
    XMolCalc is a small utility that allows you to calculate a molecular weight.
  • Xykron
    Xykron is the front end of the Chemical Resource Kit. Of the components, Xykron is the most feature-filled and provides the most diverse range of functions.
  • xyz2rgb
    xyz2rgb is a tool for animating molecules. xyz2rgb makes pretty pictures and movies of molecules. It expects input in the form of an XYZ file, one of the file formats frequently used by computational chemists. As output, it produces one or more line-interlaced RGB files.
  • YAeHMOP
    Yet Another extended Huckel Molecular Orbital Package: intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions.



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