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MBN Explorer
MBN Explorer (MesoBioNano Explorer) is a software package for molecular dynamics simulations, Energy minimization, structure optimization and kinetic Monte Carlo simulations. It is designed for Multiscale modeling, multiscale computational analysis of structure and dynamics of Cluster (physics), atomic clusters and nanoparticles, biomolecules and nanosystems, nanostructured materials, different states of matter and various interfaces. The software has been developed by MBN Research Center. History MBN Explorer inherited the experience obtained on the development of the software package Cluster Searcher. It started around 2000 as a classical molecular dynamics code for simulating many-body systems interacting via the Morse and the Lennard-Jones potentials. A variety of interatomic potentials and the possibility to combine a group of atoms into rigid blocks were introduced in 2005–2007. The first version of MBN Explorer was released in 2012 as a multipurpose computer code allowin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cross-platform
In computing, cross-platform software (also called multi-platform software, platform-agnostic software, or platform-independent software) is computer software that is designed to work in several computing platforms. Some cross-platform software requires a separate build for each platform, but some can be directly run on any platform without special preparation, being written in an interpreted language or compiled to portable bytecode for which the interpreters or run-time packages are common or standard components of all supported platforms. For example, a cross-platform application may run on Microsoft Windows, Linux, and macOS. Cross-platform software may run on many platforms, or as few as two. Some frameworks for cross-platform development are Codename One, Kivy, Qt, Flutter, NativeScript, Xamarin, Phonegap, Ionic, and React Native. Platforms ''Platform'' can refer to the type of processor (CPU) or other hardware on which an operating system (OS) or application runs, t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Interatomic Potential
Interatomic potentials are mathematical functions to calculate the potential energy of a system of atoms with given positions in space.M. P. Allen and D. J. Tildesley. Computer Simulation of Liquids. Oxford University Press, Oxford, England, 1989.R. Lesar. Introduction to Computational Materials Science. Cambridge University Press, 2013. Interatomic potentials are widely used as the physical basis of molecular mechanics and molecular dynamics simulations in computational chemistry, computational physics and computational materials science to explain and predict materials properties. Examples of quantitative properties and qualitative phenomena that are explored with interatomic potentials include lattice parameters, surface energies, interfacial energies, adsorption, cohesion, thermal expansion, and elastic and plastic material behavior, as well as chemical reactions.N. W. Ashcroft and N. D. Mermin. Solid State Physics.Saunders College, Philadelphia, 1976.Charles Kittel. Introduct ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry
Computational chemistry is a branch of chemistry that uses computer simulation 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. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials. Examples of such properties are structure (i.e., the expected positions of the constituent atoms), absolute and relative (interaction) energies, electronic charge density distributions, dipoles and higher multipole moments, vi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics Software
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and ''molecule'' is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H2O). In the kinetic theory of gases, the term ''molecule'' is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically not considere ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LAMMPS
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software, distributed under the terms of the GNU General Public License. LAMMPS was originally developed under a Cooperative Research and Development Agreement (CRADA) between two laboratories from United States Department of Energy and three other laboratories from private sector firms. , it is maintained and distributed by researchers at the Sandia National Laboratories and Temple University. Features For computing efficiency, LAMMPS uses neighbor lists (Verlet lists) to keep track of nearby particles. The lists are optimized for systems with particles that repel at short distances, so that the local density of particles never grows too large. On parallel computers, LAMMPS uses spatial-decomposition techniques to partition the simulatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NAMD
Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model. It is noted for its parallel efficiency and is often used to simulate large systems (millions of atoms). It has been developed by the collaboration of the Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL) at the University of Illinois at Urbana–Champaign. It was introduced in 1995 by Nelson ''et al.'' as a parallel molecular dynamics code enabling interactive simulation by linking to the visualization code VMD. NAMD has since matured, adding many features and scaling beyond 500,000 processor cores. NAMD has an interface to quantum chemistry packages ORCA and MOPAC, as well as a scripted interface to many other quantum packages. Together with Visual Molecular Dynamics (VMD) and QwikMD, NAMD's interface provides access to hybrid QM/MM simula ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Software For Nanostructures Modeling
This is a list of computer programs that are used to model nanostructures at the levels of classical mechanics and quantum mechanics. Furiousatoms- a powerful software for molecular modelling and visualization * Aionics.io - a powerful platform for nanoscale modelling * Ascalaph Designer * Atomistix ToolKit and Virtual NanoLab * CoNTub * CP2K * CST Studio Suite * Deneb – graphical user interface (GUI) for SIESTA, VASP, QE, etc., DFT calculation packages * Exabyte.io - a cloud-native integrated platform for nanoscale modeling, supporting simulations at multiple scales, including Density Functional Theory and Molecular Dynamics * JCMsuite – a finite element analysis software for simulating optical properties of nanostructures *LAMMPS – Open source molecular dynamics codeMAPS- Graphical user interface to build complex systems (nanostructures, polymers, surfaces...), set up and analyze ab-initio (Quantum Espresso, VASP, Abinit, NWChem...) or classical (LAMMPS, Towhee) simulati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comparison Of Software For Molecular Mechanics Modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations. See also *Car–Parrinello molecular dynamics *Comparison of force-field implementations *Comparison of nucleic acid simulation software *List of molecular graphics systems *List of protein structure prediction software *List of quantum chemistry and solid-state physics software * List of software for Monte Carlo molecular modeling * List of software for nanostructures modeling *Molecular design software *Molecular dynamics *Molecular modeling on GPUs *Molecule editor A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, v ... Notes and references External linksSINCRIS [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ultrarelativistic Limit
In physics, a particle is called ultrarelativistic when its speed is very close to the speed of light . The expression for the relativistic energy of a particle with rest mass and momentum is given by :E^2 = m^2 c^4 + p^2 c^2. The energy of an ultrarelativistic particle is almost completely due to its momentum (), and thus can be approximated by . This can result from holding the mass fixed and increasing to very large values (the usual case); or by holding the energy fixed and shrinking the mass to negligible values. The latter is used to derive orbits of massless particles such as the photon from those of massive particles (cf. Kepler problem in general relativity). In general, the ultrarelativistic limit of an expression is the resulting simplified expression when pc \gg mc^2 is assumed. Or, similarly, in the limit where the Lorentz factor \gamma = 1/\sqrt is very large (\gamma \gg 1). Expression including mass value While it is possible to use the approximation E ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Euler's Equations (rigid Body Dynamics)
In classical mechanics, Euler's rotation equations are a vectorial quasilinear first-order ordinary differential equation describing the rotation of a rigid body, using a rotating reference frame with angular velocity ω whose axes are fixed to the body. Their general vector form is : \mathbf \dot + \boldsymbol\omega \times \left( \mathbf \boldsymbol\omega \right) = \mathbf. where ''M'' is the applied torques and ''I'' is the inertia matrix. The vector \boldsymbol\alpha=\dot is the angular acceleration. In orthogonal principal axes of inertia coordinates the equations become : \begin I_1\,\dot_ + (I_3-I_2)\,\omega_2\,\omega_3 &= M_\\ I_2\,\dot_ + (I_1-I_3)\,\omega_3\,\omega_1 &= M_\\ I_3\,\dot_ + (I_2-I_1)\,\omega_1\,\omega_2 &= M_ \end where ''Mk'' are the components of the applied torques, ''Ik'' are the principal moments of inertia and ω''k'' are the components of the angular velocity. Derivation In an inertial frame of reference (subscripted "in"), Euler's second law s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coarse-grained Modeling
Coarse-grained modeling, coarse-grained models, aim at simulating the behaviour of complex systems using their coarse-grained (simplified) representation. Coarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins, nucleic acids, lipid membranes, carbohydrates or water. In these models, molecules are represented not by individual atoms, but by "pseudo-atoms" approximating groups of atoms, such as whole amino acid residue. By decreasing the degrees of freedom much longer simulation times can be studied at the expense of molecular detail. Coarse-grained models have found practical applications in molecular dynamics simulations. Another case of interest is the simplification of a given discrete-state system, as very often descriptions of the same system at different levels of detail are possible. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
