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d3web is a free, open-source platform for knowledge-based systems (expert systems). Its core is written in Java using XML and/or Office-based formats for the knowledge storage. All of its components are distributed under the terms of the Lesser General Public Licence ( LGPL ).
Free open source: ms-2.de: OpenMM: No No Yes Yes Yes Yes No Yes Yes High Performance MD, highly flexible, Python scriptable Free open source MIT: OpenMM: Orac: No No Yes Yes No Yes No Yes No Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level Free open source: Orac download page ...
Force-directed graph drawing algorithms assign forces among the set of edges and the set of nodes of a graph drawing.Typically, spring-like attractive forces based on Hooke's law are used to attract pairs of endpoints of the graph's edges towards each other, while simultaneously repulsive forces like those of electrically charged particles based on Coulomb's law are used to separate all pairs ...
The OPLS (Optimized Potentials for Liquid Simulations) force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University, and is being further developed commercially by Schrödinger, Inc.
For a system of particles with masses , with coordinates = that constitute a time-dependent random variable, the resulting Langevin equation is [2] [3] ¨ = ˙ + (), where () is the particle interaction potential; is the gradient operator such that () is the force calculated from the particle interaction potentials; the dot is a time derivative ...
CHARMM also includes polarizable force fields using two approaches. One is based on the fluctuating charge (FQ) model, also termed Charge Equilibration (CHEQ). [13] [14] The other is based on the Drude shell or dispersion oscillator model. [15] [16] Parameters for all of these force fields may be downloaded from the Mackerell website for free. [17]
The net electrostatic force acting on a charged particle with index contained within a collection of particles is given as: = ^; =where is the spatial coordinate, is a particle index, is the separation distance between particles and , ^ is the unit vector from particle to particle , () is the force magnitude, and and are the charges of particles and , respectively.
Schematic of D2Q9 lattice vectors for 2D Lattice Boltzmann. Unlike CFD methods that solve the conservation equations of macroscopic properties (i.e., mass, momentum, and energy) numerically, LBM models the fluid consisting of fictive particles, and such particles perform consecutive propagation and collision processes over a discrete lattice.