| Repository | |
|---|---|
| Written in | C++ |
| Operating system | Windows, Linux |
| Available in | English |
| Type | Chemoinformatics |
| License | GPL 2.0 |
Molsketch is a molecule editor for 2D computer graphics published as free software. [1] It is written in C++ with the Qt toolkit for Microsoft Windows and Linux. [2]
Computational chemistry is a branch of chemistry that uses computer simulations to assist in solving chemical problems. It uses methods of theoretical chemistry incorporated into computer programs to calculate the structures and properties of molecules, groups of molecules, and solids. The importance of this subject stems from the fact that, with the exception of some relatively recent findings related to the hydrogen molecular ion, achieving an accurate quantum mechanical depiction of chemical systems analytically, or in a closed form, is not feasible. The complexity inherent in the many-body problem exacerbates the challenge of providing detailed descriptions of quantum mechanical systems. While computational results normally complement information obtained by chemical experiments, it can occasionally predict unobserved chemical phenomena.
GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on central processing units (CPUs) and graphics processing units (GPUs). It is free, open-source software released under the GNU Lesser General Public License (LGPL).
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge.
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit, or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons.
Psi is an ab initio computational chemistry package originally written by the research group of Henry F. Schaefer, III. Utilizing Psi, one can perform a calculation on a molecular system with various kinds of methods such as Hartree-Fock, Post-Hartree–Fock electron correlation methods, and density functional theory. The program can compute energies, optimize molecular geometries, and compute vibrational frequencies. The major part of the program is written in C++, while Python API is also available, which allows users to perform complex computations or automate tasks easily.
A molecule editor is a computer program for creating and modifying representations of chemical structures.
Massively Parallel Quantum Chemistry (MPQC) is an ab initio computational chemistry software program. Three features distinguish it from other quantum chemistry programs such as Gaussian and GAMESS: it is open-source, has an object-oriented design, and is created from the beginning as a parallel processing program. It is available in Ubuntu and Debian.
Open-source hardware consists of physical artifacts of technology designed and offered by the open-design movement. Both free and open-source software (FOSS) and open-source hardware are created by this open-source culture movement and apply a like concept to a variety of components. It is sometimes, thus, referred to as FOSH. The term usually means that information about the hardware is easily discerned so that others can make it – coupling it closely to the maker movement. Hardware design, in addition to the software that drives the hardware, are all released under free/libre terms. The original sharer gains feedback and potentially improvements on the design from the FOSH community. There is now significant evidence that such sharing can drive a high return on investment for the scientific community.
MOPAC is a computational chemistry software package that implements a variety of semi-empirical quantum chemistry methods based on the neglect of diatomic differential overlap (NDDO) approximation and fit primarily for gas-phase thermochemistry. Modern versions of MOPAC support 83 elements of the periodic table and have expanded functionality for solvated molecules, crystalline solids, and proteins.
XDrawChem is a free software program for drawing chemical structural formulas, available for Unix and macOS. It is distributed under the GNU GPL. In Microsoft Windows this program is called WinDrawChem.
Open Babel is computer software, a chemical expert system mainly used to interconvert chemical file formats.
Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry.
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo.
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters. The code uses novel parallel algorithms and numerical methods to achieve high performance on platforms containing multiple processors, but may also be executed on a single computer.
(William) Graham Richards is a chemist and Emeritus Fellow of Brasenose College, Oxford. He served as head of the department of chemistry at the University of Oxford from 1997 to 2006.
Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture.
Python-based Simulations of Chemistry Framework (PySCF) is an ab initio computational chemistry program natively implemented in Python program language. The package aims to provide a simple, light-weight and efficient platform for quantum chemistry code developing and calculation. It provides various functions to do the Hartree–Fock, MP2, density functional theory, MCSCF, coupled cluster theory at non-relativistic level and 4-component relativistic Hartree–Fock theory. Although most functions are written in Python, the computation critical modules are intensively optimized in C. As a result, the package works as efficient as other C/Fortran-based quantum chemistry program. PySCF is developed by Qiming Sun. PySCF2.0 is the latest version of the program.
{{cite journal}}: CS1 maint: DOI inactive as of July 2024 (link)