| Original author(s) | Massimo Marchi, Piero Procacci |
|---|---|
| Developer(s) | CEA, Saclay, Paris, FR; Florence University, IT |
| Initial release | 1990 |
| Stable release | 5.4.1 / 2010 |
| Preview release | 6.0 / 2016 |
| Written in | Fortran |
| Operating system | Unix, Linux |
| Platform | IA-32, x86-64, NUMA |
| Available in | English |
| Type | Molecular dynamics |
| License | GPL |
| Website | www |
In computer software, Orac is a classical molecular dynamics program, to simulate complex molecular systems at the atomistic level. In 1989-1990, the code was written originally by Massimo Marchi during his stay at International Business Machines (IBM), Kingston (USA). In 1995, the code was developed further at the Centre européen de calcul atomique et moléculaire (CECAM). It is written in the programming language Fortran. In 1997, it was released under a GNU General Public License (GPL). [1] The latest release [2] of Orac may be run in parallel using the standard Message Passing Interface (MPI) libraries, allowing replica exchange simulations, multiple walkers metadynamics [3] simulations and multiple steered molecular dynamics [4] nonequilibrium trajectories.
Assisted Model Building with Energy Refinement (AMBER) is a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields. It is maintained by an active collaboration between David Case at Rutgers University, Tom Cheatham at the University of Utah, Adrian Roitberg at University of Florida, Ken Merz at Michigan State University, Carlos Simmerling at Stony Brook University, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals.
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia.
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed as mainly 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.
In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions.
In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both. Force fields are interatomic potentials and utilize the same concept as force fields in classical physics, with the difference that the force field parameters in chemistry describe the energy landscape, from which the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates.
Tinker, stylized as TINKER, is a computer software application for molecular dynamics simulation with a complete and general package for molecular mechanics and molecular dynamics, with some special features for biopolymers. The core of the package is a modular set of callable routines which allow manipulating coordinates and evaluating potential energy and derivatives via straightforward means.
In computational chemistry, a constraint algorithm is a method for satisfying the Newtonian motion of a rigid body which consists of mass points. A restraint algorithm is used to ensure that the distance between mass points is maintained. The general steps involved are: (i) choose novel unconstrained coordinates, (ii) introduce explicit constraint forces, (iii) minimize constraint forces implicitly by the technique of Lagrange multipliers or projection methods.
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
When examining a system computationally one may be interested in knowing how the free energy changes as a function of some inter- or intramolecular coordinate. The free energy surface along the chosen coordinate is referred to as the potential of mean force (PMF). If the system of interest is in a solvent, then the PMF also incorporates the solvent effects.
Molecular Dynamics of Mixtures (MDynaMix) is a computer software package for general purpose molecular dynamics to simulate mixtures of molecules, interacting by AMBER- and CHARMM-like force fields in periodic boundary conditions. Algorithms are included for NVE, NVT, NPT, anisotropic NPT ensembles, and Ewald summation to treat electrostatic interactions. The code was written in a mix of Fortran 77 and 90. The package runs on Unix and Unix-like (Linux) workstations, clusters of workstations, and on Windows in sequential mode.
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2003, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provides a general framework for different methods: density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) via LDA, GGA, MP2, or RPA levels of theory, classical pair and many-body potentials, semi-empirical and tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid schemes relying on the Gaussian Expansion of the Electrostatic Potential (GEEP). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method.
Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations. It provides a graphical environment for the common programs of quantum and classical molecular modelling ORCA, NWChem, Firefly, CP2K and MDynaMix . The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. Firefly covers a wide range of quantum chemistry methods. Ascalaph Designer is free and open-source software, released under the GNU General Public License, version 2 (GPLv2).
MacroModel is a computer program for molecular modelling of organic compounds and biopolymers. It features various chemistry force fields, plus energy minimizing algorithms, to predict geometry and relative conformational energies of molecules. MacroModel is maintained by Schrödinger, LLC.
Metadynamics is a computer simulation method in computational physics, chemistry and biology. It is used to estimate the free energy and other state functions of a system, where ergodicity is hindered by the form of the system's energy landscape. It was first suggested by Alessandro Laio and Michele Parrinello in 2002 and is usually applied within molecular dynamics simulations. MTD closely resembles a number of recent methods such as adaptively biased molecular dynamics, adaptive reaction coordinate forces and local elevation umbrella sampling. More recently, both the original and well-tempered metadynamics were derived in the context of importance sampling and shown to be a special case of the adaptive biasing potential setting. MTD is related to the Wang–Landau sampling.
Florian Müller-Plathe is a German theoretical chemist and professor for theoretical physical chemistry at Technische Universität Darmstadt.
Computational materials science and engineering uses modeling, simulation, theory, and informatics to understand materials. The main goals include discovering new materials, determining material behavior and mechanisms, explaining experiments, and exploring materials theories. It is analogous to computational chemistry and computational biology as an increasingly important subfield of materials science.
