Sumber: http://www.redbrick.dcu.ie/~noel/linux4chemistry/linux4chemistry.py
Berikut ini contoh software yang open source dan gratis. Insya Allah akan dimasukkan dalam rilis Kimux hydrogen yang akan datang secara bertahap. Mengingat banyaknya freesoftware yang ada maka akan dikeluarkan beberapa rilis khusus. Tunggu tanggal rilisnya.
Berikut ini contoh software yang open source dan gratis. Insya Allah akan dimasukkan dalam rilis Kimux hydrogen yang akan datang secara bertahap. Mengingat banyaknya freesoftware yang ada maka akan dikeluarkan beberapa rilis khusus. Tunggu tanggal rilisnya.
2D 
Quantum Mechanics GPL, Fortran - 2D is a numerical Hartree-Fock program for diatomic molecules.
ABINIT Quantum Mechanics GPL, Fortran - ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation).
AMMP Molecular Dynamics, Molecular Mechanics GPL, C - AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms.
AQUA 
NMR - AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy. AQUA is capable of calculating NOE violations, the level of completeness of NOEs based on the structure.
ASAD Reactions - ASAD is a software package developed for creating and integrating chemistry schemes in atmospheric models without the need to write any FORTRAN code to solve the chemical rate equations.
Ascalaph Quantum Quantum Mechanics, Molecular Mechanics, 3D Viewer GPL, C++ - Ascalaph Quantum is a GUI for preparing molecular mechanics calculations. It also provides an interface to PC GAMESS, NWChem and CP2K.
Avogadro Quantum Mechanics, Molecular Mechanics, 3D Viewer GPL, C++ - Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers a flexible rendering engine and a powerful plugin architecture.
AutoDock Docking GPL, C++ - 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. Search methods include evolutionary methods such as the Lamarckian Genetic Algorithm, in addition to the Monte Carlo simulated annealing (SA) method.
Babel Cheminformatics - Babel is a program designed to interconvert a number of file formats used in molecular modeling. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file.
B-BOP Quantum Mechanics, Molecular Dynamics, Materials GPL, C - B-BOP (Block Bond-Order Potential method) is a program for performing O(N) tight-binding (TB) calculations of molecules and bulks, based on block bond-order potential method within semi-empirical TB models. Molecular dynamics (MD) simulations for the NEV ensemble and the geometry optimization by the steepest decent (SD) method can be performed.
BIGMAC Thermodynamics GPL, Fortran - BIGMAC stands for Beyond Impressive Goals of Mechanical Artificial Computations. It uses Configurational Bias Monte Carlo (CBMC) to compute thermodynamic properties of flexible molecules. It has been used to study the adsorption behavior of linear and branched alkanes in zeolites and the vapour-liquid equilibrium of linear and branched alkanes.
Bioclipse Cheminformatics Eclipse Public License, Java - Bioclipse is a Java-based visual platform for chemo- and bioinformatics with a plugin architecture that currently includes plugins for the CDK and Jmol.
Bist 2D Draw GPL, C++ - Bist (Bidimensional Structures) is a chemical drawing program focussed on organic chemistry. Using the OpenBabel API, it can import/export in a wide variety of file formats including CML. A notable feature is that it can automatically parse linear fragments to create a 2D structure.
BKChem 2D Draw GPL, Python - BKChem is a chemical drawing program written in Python. One of its notable features is SVG export.
Bodil 3D Viewer - Bodil is a modular, multi-platform software package for biomolecular visualization and modeling. Bodil aims to provide easy three-dimensional molecular graphics closely integrated with sequence viewing and sequence alignment editing.
CACTVS Workflow - CACTVS is a distributed client/server system for the computation, management, analysis and visualisation of chemical information of any, even dynamically and ad-hoc defined type. CACTVS Tools is a visualization package for chemist.
cclib Quantum Mechanics GPL, Python - cclib (computational chemistry library) allows users to easily implement computational chemistry algorithms that use the results from calculations from any of a large number of popular computational chemistry packages (incl. GAMESS, GAMESS-UK, Jaguar, Gaussian, Molpro and ADF).
CCP1GUI Quantum Mechanics, 3D Viewer GPL, Python - CCP1GUI is a free, extensible Graphical User Interface (GUI) developed for GAMESS-UK, but also supporting other packages. The GUI has been built around the Python open-source programming language and the VTK visualisation toolkit. It has support for conventional formats such as Z-matrix and PDB, as well as programme-specific formats for CHARMM, ChemShell, XMol and Gaussian.
CDA Quantum Mechanics - CDA (Charge Decompositional Analysis) has been devised to analyze chemical systems which can be described as donor-acceptor complexes. The electronic and energetic changes associated with the formation of a complex consisting of two fragments A and B are partitioned in terms of the familiar Dewar-Chatt-Duncanson model. The energy analysis is feasible within the Hartree-Fock approximation, while the charge decomposition analysis can also be carried out at correlated levels. Requires Gaussian output files.
ChemCalc Utility - ChemCalc is intended to be a calculator oriented towards chemistry. It calculates the molecular formula, molecular mass, exact mass, elemental analysis and plots the isotopic distribution graph.
ChemicalInventory Inventory GPL, Java - ChemicalInventory is a web application that manages the chemical stock in a laboratory or production facility, where chemicals must be safely stored, easily found and tracked.
Chemistry Development Kit (CDK) Cheminformatics GPL, Java - The Chemistry Development Kit (CDK) are Java utility classes for chemoinformatics and computational chemistry. These classes include descriptor calculation, 2D structure layout, graph algorithms, and chemical file format readers among others.
ChemNomParse Cheminformatics LPGL, Java - ChemNomParse is a chemical nomenclature parser. The project aims to build molecules from an IUPAC chemical name.
ChemSol Solvation - ChemSol calculates solvation energies using the Langevin Dipoles (LD) model of the solvent and ab initio calculations.
Chemsuite 2D Draw, IR, Utility GPL, C++ - Chemsuite is composed of several programs that work independently of each other: Chem2D - a 2D molecular drawer; Molcalc - a molecular weight calculator; chemIR: an infrared spectra processor which can read, process, export and print Perkin Elmer spectra.
Chemtool 2D Draw GPL, C - Chemtool is a program for drawing organic molecules easily and store them as an X-Bitmap, Postscript and XFig file. It runs under X- Window and is written with GTK+.
CHIMP Reactions GPL, C++ - CHIMP (CHIMP Hierarchical Modeling Program) is a generic tool for the modeling of chemical phenomena. CHIMP has the ability to perform dynamic Monte Carlo simulations on chemical reactions, in particular heterogeneous catalytic reactions.
Cn3D 3D Viewer - Cn3D is a visualization tool for biomolecular structures, sequences, and sequence alignments. It can also function as a helper application for web browsers and allows the web browser to show 3-dimensional structures from NCBI's Entrez retrieval service.
Computational Crystallography Toolbox Crystallography GPL, (C++,Python) - The Computational Crystallography Toolbox (cctbx) is a collection of fundamental procedures for Computational Crystallography. It includes a unit cell toolbox , a space group toolbox and an element toolbox for the handling of scattering factors and other element properties.
CONSCRIPT Crystallography - CONSCRIPT generates Gouraud shaded isosurfaces of protein electron density for high quality presentation in journals.
CP-Optimizer Quantum Mechanics - CP-Optimizer (Counterpoise Optimizer) is an automatic procedure to perform geometry optimisation and harmonic frequency calculations using GAUSSIAN.
Dalton Quantum Mechanics - The Dalton Quantum Chemistry Program represents a powerful quantum chemistry program for the calculation of molecular properties with SCF, MP2 or MCSCF wave functions. The strengths of the program are mainly in the areas of magnetic and (frequency-dependent) electric properties, and for studies of molecular potential energy surfaces, both for static and dynamical investigations.
Debyer Crystallography GPL, C - Debyer takes a file with atom positions as input, and outputs X-ray and neutron diffraction patterns, the total scattering structure function, the pair distribution function (PDF), and related functions such as the RDF (reduced PDF). It can be used for comparison of molecular dynamics simulations or other models of atomistic structure of the material with X-ray and neutron powder diffraction experiments.
deMon2K Quantum Mechanics - deMon2K allows the user to perform ab-initio DFT calculations of large systems including transition metals with precision in a relatively short time.
DINO 3D Viewer - DINO is a realtime 3D visualization program for structural biology data. DINO aims to visualize all this structural data in a single program and to allow the user to explore relationships between the data.
DisMol 3D Viewer BSD Compatible, Java - DisMol is a molecular viewer applet written in Java, which allows molecular structures to be viewed on the web.
DRAWxtl Crystallography, 3D Viewer - DRAWxtl reads a basic description of the crystal structure, and displays it using polyhedra, planes, lone-pair cones, spheres or ellipsoids, bonds, iso-surface Fouier contours and the unit-cell boundary. Image information can be exported as Virtual Reality Modeling Language (VRML), and in a format suitable for the Persistence of Vision Ray Tracer (POV-RAY).
EasyChem 2D Draw GPL, C - EasyChem is a program designed to draw chemical structures, written under Linux and using Gtk+. Its main features are ease of drawing ornaments (non-bonding electron pairs, etc.) and EPS exporting with LaTeX fonts.
EChem++ Electrochemistry GPL, C++ - EChem++ is designed to be used for the modeling and simulation of (electro)chemical reaction kinetics as well as transport processes. Hardware control of experiments and data analysis are future aspects of the project.
Eden Crystallography GPL, C - Eden (short for Electron DENsity) implements the 'holographic' method of recovering the electron density in a crystal. The most unconventional feature of the holographic method is that it is a real-space method: it searches for a distribution of electrons in the unit cell that meets all the known constraints on the molecules themselves, while giving rise to the observed diffraction pattern.
EGO Molecular Dynamics GPL, C - EGO is a parallel program for molecular dynamics simulations of biomolecules. The program computes molecular dynamics trajectories. It uses a multiple time step algorithm combined with a structure adapted fast multipole method for the description of long range electrostatics. The method has been demonstrated to scale linearly with the number of atoms in the range of about 40,000 atoms.
Espoir Crystallography GPL, Fortran - Espoir solves crystal structures from powder diffraction data using the direct space approach.
FHI98md Quantum Mechanics - FHI98md is an efficient code to perform density functional theory total-energy calculations for materials ranging from insulators to transition metals. The package employs first-principles pseudopotentials, and a plane-wave basis-set.
FIRM NMR - FIRM (Full Iterative Relaxation Matrix) a flexible program for calculating NOEs and back-calculated distance constraints using the full relaxation matrix approach.
fityk Crystallography, Spectroscopy GPL, C++ - fiytk is a tool for curve fitting and data analysis (e.g. baseline correction), used in crystallography, chromatography, photoluminescence or photoelectron spectroscopy, infrared or Raman spectroscopy, and in other fields. Common tasks can be automated with scripts.
FlexV 3D Viewer, Docking - FlexV is a general-purpose molecular viewer. It is a stand-alone tool with easy interfaces, and can be used in combination with any kind of molecular modeling software, although originally designed as a visualisation front-end for FlexX.
FOX Crystallography GPL, C++ - FOX performs ab initio crystal structure solution from diffraction data (mostly powder diffraction data). Solutions can be constrained using angle or atom based constraints. Multiple powder patterns can be used simultaneously, and input is using a graphical user interface.
Frowns Cheminformatics Python Software Foundation License, Python - Frowns is a chemoinformatics toolkit geared toward rapid development of chemistry-related algorithms.
Gabedit Quantum Mechanics, 3D Viewer BSD-like, C - Gabedit is a graphical user interface for Molpro, Molcas, MPQC and Gaussian written in C,and based on GTK+.
GAMESS Quantum Mechanics - The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. Briefly, GAMESS can compute wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections available for some of these. Analytic gradients are available for these SCF functions, for automatic geometry optimization, transition state searches, or reaction path following.
GAMGI 3D Viewer (GPL,BSD), (C,Python,Perl) - GAMGI (General Atomistic Modelling Graphic Interface) is an object-oriented program aiming to handle all aspects directly related with building, viewing and analysing atomic strucures, such as molecules, crystals, glasses, liquids, etc.
GAMMA NMR - GAMMA is a C++ library written for simulation of Magnetic Resonance experiments. Its purpose is to provide a simple and intuitive means with which users may construct simulation programs to suit their individual needs. A Python wrapper is also available.
garlic 3D Viewer GPL, C - Garlic is a free molecular visualization program written for both educational and professional research purposes.
GaussSum Quantum Mechanics, Utility GPL, Python - GaussSum is a GUI application that can analyse the output of Gaussian 98/03, ADF, GAMESS (US), GAMESS (UK), and PC-GAMESS calculations to extract and calculate useful information. This includes the progress of the SCF cycles, geometry optimisation, UV-Vis/IR/Raman spectra, MO levels, MO contributions and more.
GChemPaint 2D Draw GPL, C++ - GChemPaint is a 2D chemical structures editor for the Gnome-2 desktop. GChemPaint is a multi document application and is a bonobo server so that chemistry can be embedded in other Gnome applications.
GDIS Crystallography, 3D Viewer GPL, C - GDIS (GTK Display Interface for Structures) is a visualization program for small molecules, crystals, and solution cells. It has support for common crystallographic file formats, and assorted tools for visualization (including diffraction pattern generation), manipulation, and model creation. Rendering of molecules and energy minimization are also possible via Povray and GULP.
gdpc 3D Viewer, Molecular Dynamics GPL, C - gdpc is a program for visualising MD simulations. It is a very versatile program and could easily be used for other purposes. gdpc reads xyz input and custom formats and can write out pictures of the frames.
gElemental Cheminformatics, Education, Periodic Table GPL, (C++, Python) - gElemental is a periodic table viewer derived from GPeriodic that provides detailed information on the chemical elements. It uses the GTK+ toolkit and is available for Linux and other GTK+ platforms. It also provides Python bindings to the data, which is stored in a separate data library.
GenChemLab Education GPL, C++ - GenChemLab (General Chemistry Lab Simulator) is a graphical application for simulating several common general chemistry exercises. It is meant to be used to help students prepare for actual lab experience.
Ghemical Quantum Mechanics, 3D Viewer GPL, C++ - Ghemical is a computational chemistry software package with GUIs for both GLUT and GTK+, and some nice 3D-visualization tools. It can do "all atoms" molecular mechanics and dynamics, as well as quantum mechanics (ab initio and semi-empirical) models. It hopefully offers a good framework for a generic freeware molecular modeling tool.
Ghemical-GMS Quantum Mechanics, 3D Viewer GPL, C++ - Ghemical-GMS is a specialized version of Ghemical developed for GAMESS. Ghemical-GMS contains an extra set of menus for creating GAMESS input files, and allows for the submission and queuing of GAMESS jobs using the GTK-Gamess program.
Gnome Chemistry Utils 3D Viewer, UItilities LGPL, C++ - The Gnome Chemistry Utils provide C++ classes and Gtk+-2 widgets related to chemistry. They are used both both in Gnome Crystal and GChemPaint.
Gnome Crystal Crystallography, 3D Viewer GPL, C++ - Gnome Crystal is a lightweight model visualiser for crystal structures.
Gnu Xtal System Crystallography GPL, Fortran - The Gnu Xtal System is a package of over sixty crystallographic programs for calculations ranging from the reduction of raw diffraction intensities, to the solution, refinement and publication of crystal structures. These are applicable to X-ray, neutron and electron diffraction analyses, including charge density studies. The package contains interactive graphics tools.
gOpenMol Quantum Mechanics, 3D Viewer, Molecular Dynamics - gOpenMol is a graphics interface to the OpenMol set of programs, but can also be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials from many programs.
GPeriodic Periodic table GPL, C - GPeriodic is a periodic table application for Linux. It allows you to browse through a periodic table of the elements and view detailed information on each of the elements on each of the elements. 118 elements are currently listed.
GRAMM Docking - GRAMM (Global Range Molecular Matching) is a program for protein-protein and protein-ligand docking. To predict the structure of a complex, it requires only the atomic coordinates of the two molecules. The program performs an exhaustive 6-dimensional search through the relative translations and rotations of the molecules.
GRINSP Crystallography GPL, Fortran - GRINSP is a Monte Carlo code (FORTRAN) for the prediction of inorganic structures built up from defined polyhedra.
GROMACS Molecular Dynamics GPL, (C, assembly, Fortran) - GROMACS is a versatile package for performing molecular dynamics. Some features of the software: standard MD simulations, energy minimizations, NMR refinement using NOE data, high performance due to well optimized code and smart algorithms, automatic topology generation from a building block library, flexible force field usage, non-equilibrium MD, many analysis and preprocessing tools.
GTK-Gamess Quantum Mechanics, 3D Viewer GPL, C++ - GTK-Gamess is a frontend to GAMESS that allows users to queue up GAMESS calculations and run them sequentially.
HONDOPLUS Molecular Dynamics - HONDOPLUS is a version of HONDO 99.6 with additional modules for evaluating Löwdin and CM2 partial atomic charges and for carrying out SM5.42R continuum solvation calculations by Hartree-Fock and hybrid DFT-Hartree-Fock methods.
ICM Browser 3D Viewer - ICM Browser is a program for molecular modeling and high-performance molecular visualization and animation. A commercial version, ICM Browser Pro, has additional capabilities relating to creating, storing and sharing structural, biological and chemical information.
Indigo Cheminformatics GPL, C++ - Indigo is a cheminformatics toolkit that includes a rendering library (Dingo), generation of canonical SMILES (Cano), an Oracle cartidge for searching molecular databses (Bingo) and R-Group deconvolution (Deco). It also can handle nucleotides (Nucleo).
Isotopic Pattern Calculator Mass Spectrometry GPL, C - Isotopic Pattern Calculator is a small tool for mass spectrometry. It calculates the isotopic distribution for a given chemical formula or peptide sequence. Furthermore, it can use Gnuplot to visualise the results.
Jana2000 Crystallography - Jana2000 is a system for solving and refinement of regular, modulated and composite structures from monocrystal and powder diffraction data.
JChemPaint 2D Draw LGPL, Java - JChemPaint is a Java program for drawing 2D chemical structures. It can load and save in CML format, export as bitmap and SVG, and automatically layout structures.
JMap3D 3D Viewer - JMap3d takes volumetric data (particularly electron density data) and polygonises them, in order to produce up to five iso-surfaces. The result is written to a VRML97 (VRML2.0) file, which can then be viewed with any VRML viewer of your choice or with the included Java3D VRML viewer (from the Java3D & VRML working group).
JME Molecular Editor 2D Draw - JME Molecular Editor is a Java applet which allows to draw / edit molecules and reactions (including generation of substructure queries) and to depict molecules directly within an HTML page. Editor can generate SMILES or MDL mol file of created structures.
Jmol 3D Viewer, Quantum Mechanics LGPL, Java - Jmol is a Java-based molecule viewer that has been developed as a cross-platform replacement for the Chime plugin. Available as an applet for web pages or as a stand-alone application. It can read multiple file formats, create animations, show molecular vibrations, and supports the Chime scripting language.
JMolEditor 3D Viewer, Quantum Mechanics - JMolEditor is a Java-based molecular viewer for quantum chemistry calculations, with support for Gaussian, GAMESS, ADF and Q-Chem calculations. Molecules can be built, and input files can be prepared and submitted. Calculation results, including isosurfaces from cube files, can be displayed.
JOELib Cheminformatics GPL, Java - JOELib is a Java library for cheminformatics. Among its many features, it can perform SMARTS substructure searches, calculate descriptors, and read and write molecular file formats including Chemical Markup Language.
JSV 3D Viewer, Crystallography - JSV (Java Structure Viewer) is a crystal structure viewer written in Java. It can also calculate X-ray diffraction intensities. The diffraction viewer module XRDL allows the 3D/2D display of the diffraction pattern. This software is 'Charityware'.
Kalzium Education, Periodic Table GPL, C++ - Kalzium is an application which will show you some information about the periodic system of the elements. It is included in KDE 3.1. A balanced equation solver, eqchem, is also part of Kalzium.
Kemistry 2D Draw, 3D Viewer, Utility GPL, C++ - Kemistry is a collection of chemistry-related applications written for the KDE2. The Kemistry package provides three applications: KMolCalc - a molecular weight calculator; KDrawStruct - a 2D structures editor; KMolViewer - a 3D molecular renderer. All Kemistry applications are still in their early development stages.
KMol Utility GPL, C++ - KMol is a molecular weight and elemental composition calculator for KDE.
KMovisto 3D Viewer GPL, C++ - KMovisto is a molecular viewer. It can import GAUSSIAN 94 or 98 files, and XYZ files. 3D view modes (anaglyph or stereo pair) make it possible to enjoy stereoscopic impressions of the molecular structure. In addition, KMovisto can export export POV-Ray files for rendering high quality presentations, as well as VRML files for 3D presentations on the world wide web.
KryoMol 3D Viewer, Quantum Mechanics, Molecular Mechanics, Molecular Dynamics, NMR GPL, C++ - KryoMol is a KDE-based program for visualisation and analysis of several chemistry related file types such as quantum chemistry log files (Gaussian, NWChem, ACESII, GAMESS), molecular mechanics log files (Tinker, Macromodel), 1-D NMR spectra and JCAMP-DX spectra.
LAMMPS Molecular Dynamics GPL, C++ - LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics (MD) code created for simulating molecular and atomic systems such as proteins in solution, liquid-crystals, polymers, zeolites, or simple Lennard-Jonesium.
LaTeX Chemistry Packages LaTeX - Chemistry packages for using with the document typesetting system LaTeX. Includes packages for reactions, molecular formulae, R and S codes, chemistry journals, symmetry elements and even to draw chemical structures.
LaueX Crystallography - LaueX is an interactive program with a GUI that can simulate a Laue diagram, when given the orientation of the crystal and the cell parameters. LaueX can also index a Laue diagram if the position of experimental spots are provided.
Lennard-Jones Gas Simulation Gas simulation GPL, C++ - The Lennard-Jones Gas Simulator does a molecular simulation of noble gases.
LSD Software NMR, Utility GPL, C - The goal of LSD (Logic for Structure Determination) is to help the user propose one or more molecular structures from data that is mainly extracted from 2D NMR spectra.
Marvin Cheminformatics, 2D Draw - Marvin is a suite of Java based chemistry software that have different forms: 1. Marvin Applets are made for the Web Developer who builds chemistry-related World Wide Web sites; 2. Marvin Beans are made for the Software Developer who wants to incorporate molecule drawing or visualizing capabilities into his/her application; 3. MarvinSketch is an application for the Chemist or anyone else who wants to draw chemical structures.
massXpert Mass spectrometry GPL, C++ - massXpert lets users analyse/predict mass spectrometric data on (bio)polymers. Notable features include ex nihilo polymer chemistry definitions, highly sophisticated editing of polymer sequences and chemical reaction simulations.
MAUD Crystallography - MAUD (Material Analysis Using Diffraction) is a general diffraction/reflectivity analysis program mainly based on the Rietveld method. It has a GUI, and a wide range of features including ab initio structure solution, various optimisation algorithms, Le Bail fitting and microstruture analysis.
MCCCS Towhee Molecular Dynamics GPL, (C, Fortran) - MCCCS Towhee is a Monte Carlo molecular simulation code which can be used for the prediction of fluid phase equilibria using a wide variety of atom-based force fields and several ensembles (Gibbs, Canonical, Isobaric-isothermal and Grand Canonical). It has also been extended for use with solid (or porous) phases.
McMaille Crystallography GPL, Fortran - McMaille is a program for indexing powder diffraction patterns by Monte Carlo and grid search.
MCTDH Quantum Mechanics - MCTDH (Multi Configuration Time Dependent Hartree) is a general algorithm to solve the time-dependent Schrödinger equation for multidimensional dynamical systems consisting of distinguishable particles. MCTDH can thus determine the quantal motion of the nuclei of a molecular system evolving on one or several coupled electronic potential energy surfaces. MCTDH can also be used to propagate density operators and to determine eigenvalues and eigenstates of a molecular vibrational Hamiltonian.
MDTools Molecular Dynamics - MDTools is a collection of programs, scripts, and utilities to make various molecular dynamics tasks easier, and to provide basic code and utilities which can be built up into larger toolsets.
Mercury Crystallography, 3D Viewer - Mercury is a program for visualising crystal structures in three dimensions. Its features include:The ability to load hit lists from ConQuest searches, or to browse the entire Cambridge Structural Database, or to read in crystal structures in various formats. The ability to rotate and translate the 3D crystal-structure display, and to view down cell axes, reciprocal cell axes, and the normals to least-squares and Miller planes. The ability to measure and display distances, angles and torsion angles by atom picking and much more.
MetaStudio Quantum Mechanics, 3D Viewer GPL, Java - MeTA Studio is programmable IDE tailored for a computational chemist. It has support for BeanShell and Jython, and integrates Jmol.
MEXICO NMR GPL, C - MEXICO simulates the NMR lineshapes of coupled spin systems undergoing chemical exchange. It will simulate systems and, if experimental data are available, it will perform an iterative fit to give optimized values of the parameters.
MMTK Molecular Dynamics CeCILL, Python - MMTK (the Molecular Modelling Toolkit) is a program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations.
ModelFree NMR GPL, Fortran - ModelFree is a program for optimizing Lipari-Szabo model free parameters to heteronuclear NMR spin relaxation data.
MOLDA for Protein Modeling 3D Viewer, Quantum Mechanics - MOLDA is a molecular modeling program. 3D molecular structures in VRML and POV-Ray formats can be generated using the output from a variety of computational chemistry programs.
Moldy Molecular Dynamics GPL, C - Moldy is a general-purpose molecular dynamics simulation program. It is sufficiently flexible that it ought to be useful for a wide range of simulation calculations of atomic, ionic and molecular systems.
Molegro Molecular Viewer 3D Viewer - Molegro Molecular Viewer is a free cross-platform application for visualization of molecules and analysis of protein-ligand interactions.
MOLEKEL 3D Viewer, Quantum Mechanics - MOLEKEL is an interactive, three-dimensional molecular graphics package. MOLEKEL represents molecules,it can superimpose molecules, calculates and displays isosurfaces of electron and spin densities as well as molecular orbitals from the output of various electronic structure calculation programs. MOLEKEL can animate and display vibrational modes, animate geometry optimizations and multiple coordinate PDB and XYZ files.
Mollie Database GPL, Perl - Mollie is a small web-oriented database for molecular information. It uses Perl for CGI, and PostgreSQL.
MOLMOL 3D Viewer - MOLMOL is a program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.
molsKetch 2D Draw GPL, C++ - molsKetch is a molecular drawing tool for 2D molecular structures. Its goal is to help you draw molecules quick and easily. As well as allowing the user to export high quality images in a number of vector and bitmap formats, it can read and write multiple chemical file formats (using the Open Babel library). molsKetch features intelligent addition/removal of hydrogen atoms and a built-in library that provides quick access to regularly used molecules and functional groups.
MolSurfer 3D Viewer, Enzyme - MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structure. MolSurfer can be used to study protein-protein and protein-DNA/RNA interfaces.
MOPAC 7 Quantum Mechanics Public Domain, Fortran - MOPAC is a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions. The semi-empirical Hamiltonians MNDO, MINDO/3, AM1, and PM3 are used in the electronic part of the calculation to obtain molecular orbitals, the heat of formation and its derivative with resperivative with respect to molecular geometry.
MOSCITO Molecular Dynamics GPL, Fortran - MOSCITO is designed for molecular dynamics simulations of condensed phase systems defined by classical molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS.
MPQC Quantum Mechanics LGPL, C++ - MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. It runs on a wide range of architectures ranging from individual workstations to symmetric multiprocessors to massively parallel computers. Its design is object oriented, using the C++ programming language.
MSMS Molecular surface - MSMS stands for Michel Sanner's Molecular Surface, or Maximal Speed Molecular Surface. It allows the user to compute very efficiently triangulations of solvent excluded surfaces.
Music Molecular Dynamics GPL, Fortran - Music (Multi-purpose SImulation Code) is an object-oriented package intended to perform various types of Molecular Dynamics and Monte Carlo simulations with user-specified forcefields. It can be used to simulate diffusion and adsoprtion in zeolites, for liquid and gas simulations as well, and may be easily extended for solid simulations.
NAB Molecular Dynamics, Molecular Mechanics GPL, C - NAB (Nucleic Acid Builder) is a computer language (specified through lex and yacc) that allows nucleic acid structures to be described in a hierarchical fashion, using a language similar to C or awk, but designed especially for the manipulation of nucleic acid structures.
NAMOT 3D Viewer - NAMOT (Nucleic Acid MOdeling Tool) is a graphic tool to build and manipulate nucleic acid structures.
nMOLDYN Molecular Dynamics CeCILL, Python - nMOLDYN is an interactive analysis program for Molecular Dynamics simulations. It is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities.
NMRPipe NMR - The NMRPipe software package consists of a series of standalone programs such as NMRPipe (spectrometer data conversion, advanced multidimensional data processing), NMRDraw (graphical interface for most package tools, interactive processing, script editing interface, time domain data inspection, real-time phasing, automated peak detection, spectral analysis), NMRWish (custom version of Tcl/Tk for spectral analysis, spectral database engine, communication between applications), DC (dipolar coupling and chemical shift analysis) and a multitude of spectral analysis tools.
NMR-SHARC NMR, Quantum Mechanics, Cheminformatics - NMR-SHARC is a cooperative, platform-independent, program-independent archving system for ab initio NMR chemical shift calculations.
NMRShiftDB server NMR, Cheminformatics GPL, Java - The NMRShiftDB server is open source software which can be used to maintain a local repository of the results of NMR experiments. This software was developed for the NMRShiftDB database, an open-source, open-access, open-submission, open-content web database for chemical structures and their associated nuclear magnetic resonance data.
NMRViewJ NMR - NMRViewJ is a program for the visualization and analysis of NMR datasets. Some of its features are: unlimited number of spectral windows and data files; contour and 1D vector plots of any plane of any 2, 3, or 4 dimensional spectra; automatic peak picking, searching, facilitated analysis and interactive peak editing; powerful command language and programmable user interface; NOE constraint generation and analysis.
NWChem Quantum Mechanics ECL, (Fortran, C, C++) - NWChem is a computational chemistry package designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources.
O 3D Viewer, Crystallography - O is a general purpose macromolecular modelling environment. The program is aimed at scientists with a need to model, build and display macromolecules, particularly in the context of crystallography..
Olex2 3D Viewer, Crystallography - Olex2 is an easy-to-use program for small-molecule structure solution and refinement. It also includes many useful tools for structure analysis, archiving and report generation. All aspects of the structure determination and publication process are presented in a single, workflow-driven package - with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.
Open Babel Cheminformatics GPL, (C++, Perl, Python, Java, Ruby) - Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. It provides a command-line interface (babel), a programming library (libopenbabel), as well as bindings to several languages such as Python, Perl, Ruby and Java.
open enventory Cheminformatics AGPL, (Javascript, PHP) - open enventory is an integrated laboratory journal and inventory program. It is a web application that runs in your browser. Automatic acquisition of freely accessible data from online databases makes manual data acquisition and catalogue searches obsolete, and price surveys can be done with a mouseclick. The laboratory journal uses the information available in the inventory database and makes the data available for all members of a workgroup. Both inventory and laboratory journal have the ability to allow data exchange between workgroups.
OpenMX Quantum Mechanics, Materials GPL, C - OpenMX (Open source package for Material eXplorer) is a program for nano-scale material simulations, which is designed for the realization of large-scale ab initio calculations based on a density functional theory (DFT) , norm-conserving pseudopotentials, and pseudo atomic localized basis functions.
OpenThermo Thermodynamics GPL, C++ - 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. In contrast to statistical subprograms integrated to QC packages, OpenThermo is designed to make the calculation transparent to user and give maximum control under the choice of used theories and approximations.
ORAC Molecular Dynamics GPL, Fortran - ORAC is a molecular dynamics program for running classical simulations of solvated biomolecules. Simulations can be carried out in the NVE, NPT, NHP, and NVT thermodynamic ensembles using multiple time steps integrators. Electrostatic interactions may be handled through the Smooth Particle Mesh Ewald method.
ORTEP Crystallography - ORTEP (Oak Ridge Thermal Ellipsoid Plot) is a program for drawing crystal structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoin probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites. There is also a Linux-specific Linux ORTEP page.
OS-ELN Electronic Lab Notebook - OS-ELN (Open Source Electronic Lab Notebook) will be of particular interest to Universities and Colleges needing a simple, low-cost ELN to be used by their students in classes. The system is easily and cost effectively deployed, and can be expanded and modified as needed.
OSET Reactions, Education GPL, Java - OSET (Organic Synthesis Exploration Tool) is a computer-assisted organic synthesis (CAOS) program for the retrosynthetic analysis of target molecules. Intended for educational use, as a tool for learning chemical synthetic design at undergraduate organic chemistry courses.
Packmol Molecular Dynamics - Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations. The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.
PDBCat Cheminformatics University of Illinois Open Source License, C - PDBCat can be used to manipulate and process PDB files using commonly available tools such as Perl, awk, etc.
pDynamo Molecular Dynamics, Molecular Mechanics, Quantum Mechanics CeCILL, (C, Python) - pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC), molecular mechanical (MM) and hybrid QC/MM potential energy functions.
Perl Chemistry Modules Cheminformatics, 3D Viewer Artistic License, Perl - Perl extensions for working with chemical information, for example SMILES strings, molecular file formats, creation of VRML files, conversion to internal coordinates. See also PerlMol.
PINY_MD Molecular Dynamics, Quantum Mechanics Common Public License, C - PINY_MD is capable of performing a wide variety of molecular dynamics, electronic structure, and geometry optimization calculations. Such capabilities include force-field based simulations on system ranging in complexity from simple molecular liquids and crystals to large biomolecular systems. In addition, PINY_MD can perform ab initio molecular dynamics and geometry optimization using plane-wave based generalized gradient (GGA) density functional based representations of the electronic structure combined with the Car-Parrinello propagation scheme.
POLYRATE Reactions - POLYRATE is a computer program for the calculation of chemical reaction rates of polyatomic species (and also atoms and diatoms as special cases).
PovChem 3D Viewer - PovChem is a chemical visualisation and illustration program with a graphic interface. It takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration, then exports the picture in POV-Ray format (high-quality images).
ProtoFit GPL, (Fortran, Tcl) - ProtoFit is a tool for optimization of surface protonation models from acid-base titration data. Although ProtoFit is designed with the analysis of the proton buffering behavior of surfaces in mind, it can be used equally well for other substances such as a dissolved acids that reversibly exchanges protons with water.
PWscf Quantum Mechanics GPL, Fortran - PWscf (Plane-Wave Self-Consistent Field) is 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.
PyDespike Raman, Spectra GPL, Python - PyDespike is a program to graphically process (ie. despike) Raman and other spectroscopic data. It reduces the tedium involved in removing spikes in data due to artificial background fluctuations.
PyMOL 3D Viewer Python License, (C, Lua, Python, Tcl) - PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.
PyQuante Quantum Mechanics BSD, (Python, C) - PyQuante is an open source suite of programs for developing quantum chemistry methods, written in the Python programming language, but with many rate-determining modules written in C for speed. The resulting code is easy to understand and modify, providing a well-engineered set of tools so that scientists can construct their own quantum chemistry programs without going through the tedium of having to write every low-level routine.
PyVib2 Quantum Mechanics GPL, Python - PyVib2 is a program for analyzing vibrational motion and vibrational spectra, written in pure Python. PyVib2 permits the automatic correlation of vibrational motions of molecules thereby allowing an understanding of Raman, Raman optical activity (ROA), infrared vibrational absorption (IR), and vibrational circular dichroism (VCD) spectra. Features include a Versatile representation of vibrational motions, visualization of Raman/ROA and IR/VCD generation in molecules and the production of publication quality spectra. It currently supports DALTON and Gaussian output files.
QMForge Quantum Mechanics, 3D Viewer GPL, Python - QMForge is a program to analyze the results of quantum chemistry (DFT) calculations: Gaussian 98/03, ADF, GAMESS (US), GAMESS (UK), and PC-GAMESS files are supported. The following analyses are available for user-defined molecular fragments: Mulliken, C-squared and Overlap Population analyses, Fragment and Charge Decomposition Analyses.
Qmol 3D Viewer, Molecular Dynamics - Qmol is a program for viewing molecular structures and animating molecular trajectories. It supports: display wire frame and space-filling molecular structures from a PDB file; animate molecular trajectories stored in the DCD file format; interactively measure bond lengths, bond angles and torsion angles; dynamically adjust user selected torsion angles; display atom labels.
QuteMol 3D Viewer GPL, C++ - QuteMol is an open source (GPL), interactive, high quality molecular visualization system that aims to improve clarity and provide an easier understanding of the 3D shape and structure of large molecules or complex proteins. Its features include real time ambient occlusion, depth-aware silhouette enhancement, and automatic generation of animated gifs of rotating molecules for web page animations.
QTree 3D Viewer - QTree is a program for generating CPK, Ball and Stick and worms pictures of molecules using the quad-tree algorithm. This is a relatively fast method of generating near-photographic quality images though it does not generate shadows. A sense of depth is provided by darkening atoms farther away from the viewer.
RasMol 3D Viewer GPL, C - RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.
RasMol-UCB 3D Viewer - UCB-Enhanced Rasmol is based on Rasmol 2.6 with enhancements added. These enhancements include: multiple molecules can be viewed, part of a molecule can be rotated around a bond, distances/angles can be measured and the labels displayed.
Raster3D 3D Viewer - Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing.
RedMD Molecular Dynamics GPL, (C, C++) - RedMD (Reduced Molecular Dynamics) is an open source package for molecular dynamics simulations and normal mode analysis for coarse-grained models of proteins and nucleic acids. Force fields are based on one-bead elastic network models and their extensions. The code is written in C/C++ and is parallelized.
RM1 Quantum Mechanics - RM1 (Recife Model 1) is a reparameterisation of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. It is distributed as an external file for recent versions of MOPAC, as the default model for a modified version of the public domain MOPAC, and also can be implemented in HyperChem.
RnaViz 3D Viewer GPL, (C, Tcl) - RnaViz is a user-friendly, portable, windows-type program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files.
SCHAKAL 3D Viewer Public Domain, Fortran - SCHAKAL is a FORTRAN program for the graphical representation of molecular and solid-state models.
SCORE Docking - SCORE is an empirical method for estimating the binding affinity of a protein-ligand complex with known 3D structure. SCORE uses a linear equation to describe the binding energy changes upon the binding process, which includes terms accounting for hydrogen-bonding, hydrophobic effect, and deformation effect.
SHELX-to-ORTEP Crystallography - SHELX-to-ORTEP converts SHELX output files to ORTEP format.
SIMPSON NMR GPL, C - SIMPSON is a General Simulation Program for Solid-State NMR. It features multi-pulse 1D/2D experiments on large spin-systems with input-files implemented using a simple scripting language. The program is designed to emulate a NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, rf irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition.
SIMREF Crystallography - simref is a structure refinement program for the simultaneous evaluation of several powder diffraction data sets and multiple phases per data set. With a structural model all calculated diffraction profiles are fitted to the corresponding observed diffraction profile by the method of least squares. This procedure is called Rietveld method (Rietveld, 1969 ). By the simultaneous refinement of several data sets new evaluation techniques are possible.
SimSoup Reactions GPL, C++ - SimSoup is is a graphical artificial chemistry simulator. 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.
Situs Crystallography, 3D Viewer, Docking GPL, C - Situs is an award-winning program package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering. The software supports both rigid-body and flexible docking using a variety of fitting strategies.
SketchEl 2D Draw GPL, Java - SketchEl is an interactive chemical molecule sketching tool, designed for quick and simple entry of structures. The feature set is limited to those necessary to enter a single chemical species, in a form that might be used in a cheminformatic database, representing each atom and bond as a part of a labelled graph.
SNF Quantum Mechanics GPL, (Fortran, C) - SNF has been developed for the calculation of Infrared, Raman, and VROA spectra using the harmonic approximation for the frequencies and the double harmonic approximation for the intensities. Vibrational frequencies are determined using numerical differentiation of analytical gradients of the total electronic energy, while infrared, Raman, and VROA intensities are obtained by numerical differentiation of dipole moments and (generalized) polarizability tensor components with respect to nuclear coordinates. Single point calculations are carried out using ADF, Dalton, Gaussian, Molpro or Turbomole.
Sparkle/AM1 Quantum Mechanics - 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.
Sparky NMR - Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.
SPIN NMR - SPIN calculates NMR spectra for systems of up to 9 spin 1/2 nuclei, given chemical shifts and coupling constants as inputs.
SSIA NMR - SSIA is a program for predicting the magnitude and orientation of a sterically induced alignment tensor from a solute's (protein or DNA/RNA) three-dimensional shape.
Steric GPL Compatible, C - Steric calculates the steric size of molecules about a point in terms of their cone angles and solid angles, as well as their total volumes and projected areas.
Swiss-PdbViewer 3D Viewer - Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
Symmetry Symmetry GPL, C - Symmetry is a set of C codes for automatic molecular symmetry recognition. Nothing fancy, but can be of use as an analytical or educational tool.
Tessel 3D Viewer GPL Compatible, Fortran - Tessel2 is a 3D compiler to produce crystal and molecular models, parametric surfaces and several forms of sphere tesselations. The program produces output to be rendered with POV-Ray 2 or 3, Geomview (OFF format), or any Virtual Reality renderer (VRML V1.0 format).
Tinker Molecular Dynamics - Tinker is a complete and general package for MM/MD, with some special features for polypeptides. TINKER has the ability to use any of several common parameter sets, such as AMBER, CHARMM, MM2, MM3, OPLS, and our own AMOEBA force field based upon polarizable atomic multipole electrostatics.
"Understanding Molecular Simulations" Molecular Dynamics - The FORTRAN source code of the Case Studies of the book Understanding Molecular Simulations.
VASP Data Viewer 3D Viewer, Quantum Mechanics GPL, C - VASP Data Viewer is a visualization program for examining output files generated by the quantum chemistry package VASP.
VEGA 3D Viewer, Quantum Mechanics, Molecular Dynamics GPL Compatible, C - VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules.
Viewmol 3D Viewer, Quantum Mechanics GPL, (C, Python) - Viewmol is an open source graphical front end for computational chemistry programs. It can be used to build molecules, trace a geometry optimisation or MD trajectory, show vibrations, draw IR or Raman spectra, MO energy diagrams, and much more.
WebMO Quantum Mechanics, 3D Viewer - WebMO is a WWW-based interface to Gamess, Gausssian, Molpro, Mopac, Nwchem, Qchem, and Tinker for setting up, submitting, and visualizing results of computational chemistry jobs.
XCombust Utility - Who in chemistry never experienced the following: You get your sample back from the analytical department and look shyly at the elemental analysis data - and they are way off. So what usually happens is that one tries to make the numbers fit by postulating solvent inclusion (like 1 mol of EtOH) and then get stressed out with a desktop calculator. That's where this tiny shiny utility comes into play.
XCrySDen 3D Viewer, Crystallography GPL, (Fortran, C) - XCrySDens (Crystalline Structures and Density) is a crystalline and molecular structure visualisation program, which can superimpose isosurfaces and contours onto crystalline structures and interactively rotate and manipulate them. XCrySDens also provides a (partial) graphical user interface for CRYSTAL, and a visualisation system for PWscf and WIEN2k.
XDrawChem 2D Draw GPL, (Fortran, C++) - XDrawChem is 2D molecule drawing program. Some notable features include the ability to retrieve structures from a network database given the name or CAS number; it can predict predict proton and C13 NMR shifts; and it can interface with OpenBabel to read and write multiple file formats.
xem Education GPL, C++ - xem is a simple software simulating titration for various systems.
XLOGP/PLOGP Cheminformatics - Method which can calculate the logP value for an organic compound from its topological structure. The algorithm is based on the summation of atomic contributions and correction factors.
XMakemol 3D Viewer GPL, C++ - 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.
XMD Molecular Dynamics GPL, C - XMD performs Computer Molecular Dynamics (CMD) simulations on metals and ceramics.
XmMol 3D Viewer GPL, C - XmMol is a desktop macromolecular visualization and modeling tool designed to be easy to use, configure and enhance. Its graphics are based on X11, and part of its user interface is based on Motif. Thus it provides a way of displaying structures on any X11 server.
XMolCalc Utility - XMolCalc is a small utility that allows you to calculate a molecular weight under Unix/X11.
XOrtep Crystallography - XOrtep is is a slightly modified version of the ortep-for-sun code that was written to provide an editor/previewer combination based on Sun's OpenView toolkit.
XPMA Crystallography - XPMA is a mouse driven menu based graphical program for the manipulation of crystal structures. It reads SHELX93, SHELXL, SHELX76 and SHELXS-OUTPUT FILES.
XPovChem 3D Viewer GPL, C - XPovChem is a molecule viewer based on the PovRay raytracer. It takes a molecule description, converts it into a .pov file, and lets povray render the image -- thus allowing a very high rendering quality. Xpovchem includes the professional Babel molecule format converter and is a GUI frontend to Paul Thiessen's povchem console program.
XRDL Crystallography - XRDL is reciprocal space viewer written in Java. It is also released as part of JSV. It allows real-time rotation of the reciprocal lattice points. This software is 'Charityware'.
XVibs 3D Viewer, Quantum Mechanics GPL, Java - XVibs is a utility for animating molecular vibrations. Normal modes are read from a file automatically determined to be from Aces2, Gamess, PC Gamess, Gaussian 90/92/95/94/98, ADF, Dalton, Jaguar, MOPAC, or HyperChem. Separate animation files are written for each vibration.
YAeHMOP Quantum Mechanics GPL, (C, Fortran) - Yet Another extended Huckel Molecular Orbital Package (YAeHMOP) is 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.
Yambo Quantum Mechanics GPL, (C, Fortran) - Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by the DFT codes abinit and Pwscf.
YASARA View 3D Viewer - Explore macromolecular structures interactively with YASARA View, whose innotive 3D engine is up to 35 times faster than OpenGL. You can load multiple structures at the same time, create publication-quality ray-traced images including labels, and program your own macros and Python plugins.
Zodiac GPL, C++ - Zodiac is an advanced molecular editor for molecular modelling and computer aided drug design, that offers tools such as energy minimisation, database management, molecular property prediction and front ends to various docking and QM programs. It is cross platform and released under the GPL.
ZORTEP Crystallography - ZORTEP is a mouse driven, menu based graphical ORTEP program. This allows the 'real-time' graphical rotation and manipulation of structures and/or thermal ellipsoids on the screen.
200 results found- ZORTEP is a mouse driven, menu based graphical ORTEP program. This allows the 'real-time' graphical rotation and manipulation of structures and/or thermal ellipsoids on the screen.
