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Molecular Modeling On GPUs
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations. In 2007, NVIDIA introduced video cards that could be used not only to show graphics but also for scientific calculations. These cards include many arithmetic units (, up to 3,584 in Tesla P100) working in parallel. Long before this event, the computational power of video cards was purely used to accelerate graphics calculations. What was new is that NVIDIA made it possible to develop parallel programs in a high-level application programming interface (API) named CUDA. This technology substantially simplified programming by enabling programs to be written in C/C++. More recently, OpenCL allows cross-platform GPU acceleration. Quantum chemistry calculations and molecular mechanics simulations (molecular modeling in terms of classical mechanics) are among beneficial applications of this technology. The video cards can accelerate the calculations tens of times, so a PC wi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BigDFT
BigDFT is a free software package for physicists and chemists, distributed under the GNU General Public License, whose main program allows the total energy, charge density, and electronic structure of systems made of electrons and nuclei (molecules and periodic/crystalline solids) to be calculated within density functional theory (DFT), using pseudopotentials, and a wavelet basis. Overview BigDFT implements density functional theory (DFT) by solving the Kohn–Sham equations describing the electrons in a material, expanded in a Daubechies wavelet basis set and using a self-consistent direct minimization or Davidson diagonalisation methods to determine the energy minimum. Computational efficiency is achieved through the use of fast short convolutions and pseudopotentials to describe core electrons. In addition to total energy, forces and stresses are also calculated so that geometry optimizations and ab initio molecular dynamics may be carried out. The Daubechies wavelet basis ... [...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] |
Visual Molecular Dynamics
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. History VMD has been developed under the aegis of principal investigator Klaus Schulten in the Theoretical and Computational Biophysics group at the Beckman Institute for Advanced Science and Technolog ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TINKER
Tinker or tinkerer is an archaic term for an itinerant tinsmith who mends household utensils. Description ''Tinker'' for metal-worker is attested from the thirteenth century as ''tyckner'' or ''tinkler''. Some travelling groups and Romani people specialised in the trade, and the name was particularly associated with indigenous Irish Travellers and Scottish Highland Travellers – the name of whose language '' Beurla Reagaird'' means "speech of the metalworkers".Kirk, J. & Ó Baoill, D. ''Travellers and their Language'' (2002) Queen's University Belfast However, this use is considered offensive. The term "tinker", in British English, may refer to a mischievous child. Some modern-day nomads with an English, an Irish or a Scottish influence call themselves "techno-tinkers" or "technogypsies" in a revival of sorts of the romantic view of the tinker's lifestyle. "Tinker's dam" or "damn" and "tinker's curse" Both phrases tinker's damn and tinker's curse can be applied to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TeraChem
TeraChem is a computational chemistry software program designed for CUDA-enabled Nvidia Graphics processing unit, GPUs. The initial development started at the University of Illinois at Urbana-Champaign and was subsequently commercialized. It is currently distributed by PetaChem, LLC, located in Silicon Valley. As of 2020, the software package is still under active development. Core features TeraChem is capable of fast ''Ab initio quantum chemistry methods, ab initio'' molecular dynamics and can utilize density functional theory (DFT) methods for ''Nanoscopic scale, nanoscale'' biomolecular systems with hundreds of atoms. All the methods used are based on Gaussian orbitals, in order to improve performance on contemporary (2010s) computer hardware. Press coverage * Chemical and Engineering News (C&EN) magazine of the American Chemical Society first mentioned the development of TeraChem in Fall 2008. * Recently, C&EN magazine has a feature article covering molecular modeling on GPU a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Octopus (software)
Octopus is a software package for performing KohnSham density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations. Octopus employs pseudopotentials and real-space numerical grids to propagate the KohnSham orbitals in real time under the influence of time-varying electromagnetic fields. Specific functionality is provided for simulating one-, two-, and three-dimensional systems. Octopus can calculate static and dynamic polarizabilities and first hyperpolarizabilities, static magnetic susceptibilities, absorption spectra, and perform molecular dynamics simulations with Ehrenfest and Car–Parrinello methods. The code is written predominantly in Fortran, with some C and Perl. It is released under the GPL. The latest version 12.0 was released September 19, 2022. Target problems * Linear optical (i.e. electronic) response of molecules or clusters, also second-order nonlinear response. * Non-linear response to classical high-intensity electr ... [...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] |
Firefly (computer Program)
Firefly, formerly named PC GAMESS, is an ab initio computational chemistry program for Intel-compatible x86, x86-64 processors based on GAMESS (US) sources. However, it has been mostly rewritten (60-70% of the code), especially in platform-specific parts (memory allocation, disk input/output, network), mathematic functions (e.g., matrix operations), and quantum chemistry methods (such as Hartree–Fock method, Møller–Plesset perturbation theory, and density functional theory). Thus, it is significantly faster than the original GAMESS. The main maintainer of the program was Alex Granovsky. Since October 2008, the project is no longer associated with GAMESS (US) and the Firefly rename occurred. Until October 17, 2009, both names could be used, but thereafter, the package should be referred to as Firefly exclusively. History On December 4, 2009, the support of any PC GAMESS versions earlier than the first PC GAMESS Firefly version 7.1.C was abandoned, and any and all licenses to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Desmond (software)
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. The core and source code are available at no cost for non-commercial use by universities and other not-for-profit research institutions, and have been used in the Folding@home distributed computing project. Desmond is available as commercial software through Schrödinger, Inc. Molecular dynamics program Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using particle mesh Ewald-based methods. Constraints can be enforced using the M-SHAKE algorithm. These methods can be used together with time-scale splitting (RESPA-based) inte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CP2K
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, 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 ( AM1, PM3, MNDO, MNDOd, PM6) 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). The Gaussian and Augmented Plane Waves method (GAPW) as an extension of the GPW method allows for all-electron calculations. CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition sta ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
