![]() ![]() NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Manual: HTML (accessible on local systems only).It also interfaces with Gaussian 09 for quantum chemistry calculations of small molecule ligands and NAMD for molecular dynamics. MOE 2020 from Chemical Computing, Ltd., is available for the molecular modeling of large, macromolecular systems such as proteins and nucleic acids. The free academic version of this software is currently available. It has rendering capabilities, a powerful selection of analysis tools, and an easy-to-use design combine to make Maestro a versatile modeling environment for all researchers. It provides a unified interface for all Schrodinger software. Maestro is a powerful, all-purpose molecular modeling environment. Command: There are multiple executables installed in /usr/bin for all users.It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is a package to perform molecular dynamics, i.e. Gnuplot has been supported and under active development since 1986. It is also used as a plotting engine by third-party applications like Octave. It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. The source code is copyrighted but freely distributed (i.e., you don’t have to pay for it). GnuPlot is a portable command-line driven graphing utility for Linux, Windows, and OS X. One an think of this as a “free version” of Adobe Photoshop. ![]() GIMP is an open-source, cross-platform image editor with basic image editing capabilities. Website: HTML (the newest version is Gaussian ’16, but many commands are still applicable to Gaussian ’09).The Avogadro and MOE molecular modeling software packages provide a a visualization and graphical user interface to the Gaussian ’09 engine. Starting from the fundamental laws of quantum mechanics, Gaussian ’09 predicts the energies, molecular structures, vibrational frequencies and molecular propertiesManual: of molecules and reactions in a wide variety of chemical environments. Gaussian ’09 provides state-of-the-art capabilities for electronic structure modeling and is used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. It offers flexible high quality rendering and a powerful plugin architecture. Autodock Vina significantly improves the average accuracy of the binding mode predictions compared to Autodock 4.Īvogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Autodock VinaĪutodock Vina is an open-source molecular modeling program for performing molecular docking calculations of small molecules. If this is the case, that is noted below. Some of the software packages included in this list are for various instruments in other labs operated by the Department of Chemistry. Commercial software available in the lab under a license purchased by Tennessee Tech University cannot be installed on student-owned computers due to our license agreement. Please note that any software downloaded via the internet to your own computer is installed at your own risk. Most of the free and open source software packages can be installed on student-owned computers if you wish to use it at home or on your own computer. ![]() If you require the user of a software package that is not currently installed on these systems, please contact the administrator to inquire about installing it. Some of this software is free or open source software that is installed for all users, and other software is commercial software that Tennessee Tech University has purchased for faculty, student or staff use. The workstations in the molecular modeling laboratory located in the Laboratory Science Commons - 2335 have a variety of software packages installed for molecular modeling and computational chemistry applications. ![]()
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