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Free Energy Perturbation
Free-energy perturbation (FEP) is a method based on statistical mechanics that is used in computational chemistry for computing free-energy differences from molecular dynamics or Metropolis Monte Carlo simulations. The FEP method was introduced by Robert W. Zwanzig in 1954. According to the free-energy perturbation method, the free-energy difference for going from state A to state B is obtained from the following equation, known as the ''Zwanzig equation'': : \Delta F(\mathbf \to \mathbf) = F_\mathbf - F_\mathbf = -k_\text T \ln \left\langle \exp\left(-\frac \right) \right\rangle_\mathbf, where ''T'' is the temperature, ''k''B is the Boltzmann constant, and the angular brackets denote an average over a simulation run for state A. In practice, one runs a normal simulation for state A, but each time a new configuration is accepted, the energy for state B is also computed. The difference between states A and B may be in the atom types involved, in which case the Δ''F'' obtained ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Statistical Mechanics
In physics, statistical mechanics is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities. Sometimes called statistical physics or statistical thermodynamics, its applications include many problems in a wide variety of fields such as biology, neuroscience, computer science Computer science is the study of computation, information, and automation. Computer science spans Theoretical computer science, theoretical disciplines (such as algorithms, theory of computation, and information theory) to Applied science, ..., information theory and sociology. Its main purpose is to clarify the properties of matter in aggregate, in terms of physical laws governing atomic motion. Statistical mechanics arose out of the development of classical thermodynamics, a field for which it was successful in explaining macroscopic physical properties—such as temperature, pressure, and heat capacity—in terms of microscop ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Force Field (chemistry)
In the context of chemistry, molecular physics, physical chemistry, and molecular modelling, a force field is a computational model that is used to describe the forces between atoms (or collections of atoms) within molecules or between molecules as well as in crystals. Force fields are a variety of interatomic potentials. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system on the atomistic level. Force fields are usually used in molecular dynamics or Monte Carlo simulations. The parameters for a chosen energy function may be derived from classical laboratory experiment data, calculations in quantum mechanics, or both. Force fields utilize the same concept as force fields in classical physics, with the main difference being that the force field parameters in chemistry describe the energy landscape on the atomistic level. From a force field, the acting forces on every particle are derived as a g ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tinker (software)
Tinker, previously stylized as TINKER, is a suite of computer software applications for molecular dynamics simulation. The codes provide a complete and general set of tools for molecular mechanics and molecular dynamics, with some special features for biomolecules. The core of the software is a modular set of callable routines which allow manipulating coordinates and evaluating potential energy and derivatives via straightforward means. Tinker works on Windows, macOS, Linux and Unix. The source code is available free of charge to non-commercial users under a proprietary license. The code is written in portable FORTRAN 77, Fortran 95 or CUDA with common extensions, and some C. Core developers are: (athe Jay Ponder lab at the Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri. Laboratory head Ponder is Full Professor of Chemistry, and of Biochemistry & Molecular Biophysics; (bthe Pengyu Ren lab at the Department of Biomedical Engineering Universi ... [...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] |
MacroModel
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. It performs simulations in the framework of classical mechanics, also termed ''molecular mechanics'', and can perform molecular dynamics simulations to model systems at finite temperatures using stochastic dynamics and mixed Monte Carlo algorithms. ''MacroModel'' supports Windows, Linux, macOS, Silicon Graphics (SGI) IRIX, and IBM AIX AIX (pronounced ) is a series of Proprietary software, proprietary Unix operating systems developed and sold by IBM since 1986. The name stands for "Advanced Interactive eXecutive". Current versions are designed to work with Power ISA based .... The Macromodel software package was first been described in the scientific literature in 1990, and has bee ... [...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] |
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) in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CHARMM
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. Force fields The CHARMM force fields for proteins include: united-atom (sometimes termed ''extended atom'') CHARMM19, all-atom CHARMM22 and its dihedral potential corrected variant CHARMM22/CMAP, as well as later versions CHARMM27 and CHARMM36 and various modifications such as CHARMM36m and CHARMM36IDPSFF. In the CHARMM22 protein force field, the atomic partial charges were derived from quantum chemical calculations of the interactions between model compounds and water. Furthermor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BOSS (molecular Mechanics)
Biochemical and Organic Simulation System (BOSS) is a general-purpose molecular modeling program that performs molecular mechanics calculations, Metropolis Monte Carlo statistical mechanics simulations, and semiempirical Austin Model 1 (AM1), PM3 (chemistry), PM3, and PDDG/PM3 quantum mechanics calculations. The molecular mechanics calculations cover energy minimizations, normal mode analysis and conformational searching with the Optimized Potentials for Liquid Simulations (OPLS) force fields. BOSS is developed by Prof. William L. Jorgensen at Yale University, and distributed commercially by Cemcomco, LLC and Schrödinger (company), Schrödinger, Inc. Key features * OPLS Force field (chemistry), force field inventor * Geometry optimization * Semiempirical quantum chemistry * MC simulations for pure liquids, solutions, clusters or gas-phase systems * Free energies are computed from statistical perturbation (free energy perturbation (FEP)) theory * TIP3P, TIP4P, and TIP5P water mode ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
AMBER
Amber is fossilized tree resin. Examples of it have been appreciated for its color and natural beauty since the Neolithic times, and worked as a gemstone since antiquity."Amber" (2004). In Maxine N. Lurie and Marc Mappen (eds.) ''Encyclopedia of New Jersey'', Rutgers University Press, . Amber is used in jewelry and as a healing agent in Traditional medicine, folk medicine. There are five classes of amber, defined on the basis of their chemical constituents. Because it originates as a soft, sticky tree resin, amber sometimes contains animal and plant material as Inclusion (mineral), inclusions. Amber occurring in coal seams is also called resinite, and the term ''ambrite'' is applied to that found specifically within New Zealand coal seams. Etymology The English word ''amber'' derives from Arabic from Middle Persian 𐭠𐭭𐭡𐭫 (''ʾnbl'' /ambar/, “ambergris”) via Medieval Latin, Middle Latin ''ambar'' and Middle French ''ambre''. The word referred to what is n ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bennett Acceptance Ratio
The Bennett acceptance ratio method (BAR) is an algorithm for estimating the difference in free energy between two systems (usually the systems will be simulated on the computer). It was suggested by Charles H. Bennett in 1976. Preliminaries Take a system in a certain super (i.e. Gibbs) state. By performing a Metropolis Monte Carlo walk it is possible to sample the landscape of states that the system moves between, using the equation : p(\text_x \rightarrow \text_y) = \min \left(e ^ , 1 \right) = M(\beta \, \Delta U) where Δ''U'' = ''U''(State''y'') − ''U''(State''x'') is the difference in potential energy, β = 1/''kT'' (''T'' is the temperature in kelvins, while ''k'' is the Boltzmann constant), and M(x) \equiv \min(e^ , 1) is the Metropolis function. The resulting states are then sampled according to the Boltzmann distribution of the super state at temperature ''T''. Alternatively, if the system is dynamically simulated in the canonical ensemble (al ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
