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MBN Explorer
MBN Explorer (MesoBioNano Explorer) is a software package for molecular dynamics simulations, structure optimization and kinetic Monte Carlo simulations. It is designed for multiscale computational analysis of structure and dynamics of 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 allowing to model different molecular systems of varied level of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cross-platform
Within 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 platform, 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 Interpreter (computing), interpreters or run-time packages are common or standard components of all supported platforms. For example, a cross-platform application software, application may run on Linux, macOS and Microsoft Windows. Cross-platform software may run on many platforms, or as few as two. Some frameworks for cross-platform development are Codename One, ArkUI-X, Kivy (framework), Kivy, Qt (software), Qt, GTK, Flutter (software), Flutter, NativeScript, Xamarin, Apache Cordova, Ionic (mobile app framework ... [...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. Introdu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry
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 (dihydrogen cation), 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. Overview Computational chemistry differs from theoretical chemistry, which involves a mathematical description of chem ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics Software
A molecule is a group of two or more atoms that are held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions that 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LAMMPS
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a molecular dynamics program developed by Sandia National Laboratories. It utilizes the Message Passing Interface (MPI) for parallel communication, enabling high-performance simulations. LAMMPS is a free and open-source software, distributed under the terms of the GNU General Public License. It is available on Linux, Windows, and macOS platforms. History LAMMPS was developed in the mid-1990s under a Cooperative Research and Development Agreement between two laboratories from the United States Department of Energy (Sandia National Laboratories and Lawrence Livermore National Laboratory) and three companies (Cray, DuPont, and Bristol-Myers Squibb). The goal was to create a parallel molecular dynamics code capable of running on large supercomputers for materials and biomolecular modeling. Initially written in Fortran, LAMMPS has since been rewritten in C++ to provide more flexibility and ease in adding new f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GROMACS
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) ( GPL prior to Version 4.6). History The GROMACS project originally began in 1991 at Department of Biophysical Chemistry, University of Groningen, Netherlands (1991–2000). Its name originally derived from this time (GROningen MAchine for Chemical Simulations) although currently GROMACS is not an abbreviation for anything, as little active development has taken place in Groningen in recent decades. The original goal was to construct a dedica ... [...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 (not to be confused with CHARMM). 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 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Software For Nanostructures Modeling
This is a list of notable 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 * Enalos Cloud Platform – a cloud platform containing tools for the digital construction of energy minimized nanotubes and ellipsoidal nanoparticles and the calculation of their atomistic descriptors. * 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 molecu ... [...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 *PyMOL 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 . Notations commonly used are v \approx c or \beta \approx 1 or \gamma \gg 1 where \gamma is the Lorentz factor, \beta = v/c and c is the speed of light. The energy of an ultrarelativistic particle is almost completely due to its kinetic energy E_k = (\gamma - 1) m c^2. The total energy can also be approximated as E = \gamma m c^2 \approx pc where p = \gamma m v is the Lorentz invariant momentum. This can result from holding the mass fixed and increasing the kinetic energy to very large values or by holding the energy fixed and shrinking the mass to very small values which also imply a very large \gamma. Particles with a very small mass do not need much energy to travel at a speed close to c. 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). Ultrarelativistic approximations ... [...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. They are named in honour of Leonhard Euler. In the absence of applied torques, one obtains the Euler top. When the torques are due to gravity, there are special cases when the motion of the top is integrable. Formulation 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 \dot is the angular acceleration. Again, note that all quantities are defined in the rotating reference frame. 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_ + ... [...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 possibl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
