Avogadro WebPage Avogadro Download Avogadro Manual Avogadro Tutorial Video
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.
Tinker-FFE Installer for Windows
The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Tinker has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, AMOEBA (2004, 2009, 2013, 2017, 2018) polarizable atomic multipole force fields, AMOEBA+ that adds charge penetration effects, and our new HIPPO (Hydrogen-like Interatomic Polarizable Potential) force field.
Tinker 8 is a major new release of the Ponder Lab tool set for molecular mechanics and dynamics calculations. An important change in this new version is the switch from old-style common blocks to Fortran modules. Use of modules and greatly increased use of dynamic memory allocation means Tinker can now support very large molecular systems. Tinker 8 also implements improved OpenMP parallelization throughout many parts of the code. Additional major improvements include parallel neighbor list building and updating, a big reduction in iterations needed to converge polarization via an efficient PCG solver, and the reparameterizaton of Poisson-Boltzmann and Generalized Kirkwood implicit solvation models.
Tinker is also available on Github! The TinkerTools organization has a full Github site at Github TinkerTools with complete source code for canonical Tinker and other packages in the Tinker software suite. The master repository on the Github site is updated frequently with new minor features and bug fixes. It the place to go for the latest revisions of the software. Prebuilt executables are not available via the Github site.
Tinker 9 is a reimplementation of significant portions of Tinker in C++, using OpenACC and CUDA to support NVIDIA GPU calculations. Tinker-HP is an distributed, MPI-parallel Fortran code that is also GPU capable via use of CUDA for compute intensive functions. Both of these Tinker-based codes are available from the TinkerTools Github site.
PACKMOL WebPage PACKMOL Download PACKMOL Examples
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. The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy. The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats.
VMD WebPage VMD Download VMD Tutorial Video
VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. You will need a username and password to download software.
If this is your first download, please choose a username and password to register. Current NAMD or VMD users, please enter your existing username and password.
GAMESS WebPage GAMESS Download
GAMESS is a program for ab initio molecular quantum chemistry. GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Excited states can be computed by CI, EOM, or TD-DFT procedures. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment potentials, or continuum models such as the Polarizable Continuum Model. Numerous relativistic computations are available, including infinite order two component scalar relativity corrections, with various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments. Nuclear wavefunctions can also be computed, in VSCF, or with explicit treatment of nuclear orbitals by the NEO code.
MacMolPlt WebPage MacMolPlt Download
A modern graphics program for plotting 3-D molecular structures and normal modes (vibrations). Mouse driven interface for real-time rotation and translation. Copy and paste functionality for interfacing to other programs such as word processors or other graphics programs (like ChemDraw). 3D color display with lighting and shading using OpenGL. Simple printing to color or black and white printers (publication quality). Output high quality images in a variety of both still (jpeg, gif, etc) and animated (gif, flash, etc) formats. Multiple files open at once. It reads a variety of file formats including any GAMESS input, log or IRC file directly to create animations of IRC's, DRC's, and optimizations. You may also import a $VEC group from any file (such as a GAMESS .DAT file). In addition xMol XYZ files, MolDen format files and Chemical Markup Language (CML) files are supported. Also some PDB file support and MDL MolFile support is included. Fast (multi-threaded) on the fly computation of orbitals, densities and molecular electrostatic potentials for display as 2D contour maps or 3D isosurfaces! 2D Contour maps computed live with rotations or animations! Compute orbitals across an animation. Molecular Electrostatic Potentials available either alone or color mapped to a total electron density isosurface. Ability to create density difference maps, or abitrary combinations of densities. Molecular point group symmetry is supported. You may also paste GAMESS and Gaussian-92 style cartesian coordinates directly into the program. Animation of Normal Modes. Animation of IRC's, and DRC's including orbitals. Simple Energy Plots (including geometrical parameters). Simple frequency line graph of frequency versus infrared or Raman intensity. Append multiple GAMESS files together to create a single animation. Build or modify molecules using the graphical molecule builder. Quickly build realistic 3D structures. rotate selected atoms about bonds, change bond or dihedral angles. translate and rotate selected subgroups. Build molecules from scratch using cartesian or internal coordinates. GAMESS input file (.inp) builder. Both simple to use and many advanced GAMESS features are available. Automatically include optimized orbitals from one computation into your next run! Generate input for GAMESS Effective Fragment Potential computations. Generate input for GAMESS Fragment Molecular Orbital computations.
Provides hands-on knowledge enabling students of and researchers in chemistry, biology, and engineering to perform molecular simulations.
This book introduces the fundamentals of molecular simulations for a broad, practice-oriented audience and presents a thorough overview of the underlying concepts. It covers classical mechanics for many-molecule systems as well as force-field models in classical molecular dynamics; introduces probability concepts and statistical mechanics; and analyzes numerous simulation methods, techniques, and applications.
Molecular Simulations: Fundamentals and Practice starts by covering Newton's equations, which form the basis of classical mechanics, then continues on to force-field methods for modelling potential energy surfaces. It gives an account of probability concepts before subsequently introducing readers to statistical and quantum mechanics. In addition to Monte-Carlo methods, which are based on random sampling, the core of the book covers molecular dynamics simulations in detail and shows how to derive critical physical parameters. It finishes by presenting advanced techniques, and gives invaluable advice on how to set up simulations for a diverse range of applications.
Addresses the current need of students of and researchers in chemistry, biology, and engineering to understand and perform their own molecular simulations. Covers the nitty-gritty ? from Newton's equations and classical mechanics over force-field methods, potential energy surfaces, and probability concepts to statistical and quantum mechanics. Introduces physical, chemical, and mathematical background knowledge in direct relation with simulation practice. Highlights deterministic approaches and random sampling (eg: molecular dynamics versus Monte-Carlo methods). Contains advanced techniques and practical advice for setting up different simulations to prepare readers entering this exciting field.
Molecular Simulations: Fundamentals and Practice is an excellent book benefitting chemist, biologists, engineers as well as materials scientists and those involved in biotechnology.