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Topic: Molecular dynamics

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	Molecular dynamics - Wikipedia, the free encyclopedia
		Molecular dynamics (MD) simulation is a special discipline of molecular modelling.
		In physics, MD is used to examine the dynamics of atomic-level phenomena that cannot be observed directly, such as thin film growth and ion-subplantation.
		In Big O notation, common molecular dynamics simulations usually scale by either O(nlog(n)), or with good use of neighbour tables, O(n), with n as the number of molecules.
	en.wikipedia.org /wiki/Molecular_dynamics (1606 words)

	Load balancing of molecular dynamics simulation with NWChem
		The implementation of the molecular dynamics module of NWChem is based on a domain decomposition of the chemical system, taking advantage of the distribution of data to reduce the memory requirements and the locality of intermolecular interactions to reduce the communication requirements.
		Molecular dynamics simulations are an important tool in the study and rational design of molecular systems and materials, providing information about the behavior of chemical systems that can be difficult to obtain by other means.
		The molecular dynamics module of NWChem is based on a domain decomposition approach in which all remote data access during the evaluation of atomic forces is performed by one-sided asynchronous communication operations.
	www.research.ibm.com /journal/sj/402/straatsma.html (3776 words)

	Molecular Dynamics
		Molecular dynamics is the science of simulating the motions of a system of particles.
		The essential elements for a molecular dynamics simulation are a knowledge of (1) the interaction potential (i.e., potential energy) for the particles, from which the forces can be calculated, and (2) the equations of motion governing the dynamics of the particles.
		That is, molecular dynamics is used to animate the molecular model obtained from energy minimization.
	www.biochem.vt.edu /modeling/molecular_dynamics.html (356 words)

	Molecular Dynamics
		In the broadest sense, molecular dynamics is concerned with molecular motion.
		The basic ingredients of molecular dynamics are the calculation of the force on each atom, and from that information, the position of each atom throughout a specified period of time (typically on the order of picoseconds = 10^-12 seconds).
		Molecular dynamics has no defined point of termination other than the amount of time that can be practically covered.
	cmm.info.nih.gov /modeling/guide_documents/molecular_dynamics_document.html (677 words)

	Molecular Dynamics (Site not responding. Last check: 2007-11-05)
		Molecular dynamics was initiated by Alder and Wainwright [1957].
		Another application of molecular dynamics is calculation of the Gibbs free energy using free energy perturbation theory [Bash 1987, Lybrand 1990], where atoms are slowly grown into other atoms.
		Since molecular dynamics does not permit the making and breaking of bonds, the ligands have to be bonded covalently to the bases at forehand.
	wwwcmc.pharm.uu.nl /webcmc/md/home.html (1473 words)

	Molecular Dynamics Simulations
		Molecular dynamics simulations in solvent of the glucocorticoid receptor protein in complex with a glucocorticoid response element DNA sequence.
		In preparation for molecular dynamics, we docked the GR DBD dimer at H-bonding distance within the DNA major groove halfsites of the 29 bp GRE sequence; we placed the complex in a 10 Angstrom water layer and conducted 300 picoseconds of molecular dynamics.
		The results of molecular dynamics, described herein, indicate that the GR DBD interacts with its naturally occuring cognate GRE and flanking nucleotides resulting in DNA bending, strand separation, elongation and unwinding, events which have been associated with helicase activity and transcription initiation (15).
	www.msi.umn.edu /~quantum/jbmsd.html (7642 words)

	The Amber Molecular Dynamics Package (Site not responding. Last check: 2007-11-05)
		"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
		Path integral molecular dynamics simulations can be used to sample equilibrium canonical distributions using quantum dynamics rather than Newton's equations for nuclear motion.
		H++ is a tool to estimate pKa's of protein side chains, and to automate the process of assigning protonation states for molecular dynamics simulations.
	amber.scripps.edu (2497 words)

	Highlights in Molecular Dynamics (Site not responding. Last check: 2007-11-05)
		Dynamical simulations using particles represent an indispensable tool for many areas of modern scientific research and engineering.
		In materials science, the method of molecular dynamics and related simulation techniques provide unique microscopic information that is not accessible by experimental methods.
		It this way, molecular dynamics simulation is of essential strategic importance for chemical and pharmaceutical industry as well as for metallurgy and other industries with development requiring basic research in material science.
	www.nada.kth.se /~fzet/ITM/workshop (548 words)

	Molecular Dynamics
		The Molecular Dynamics section conducts basic and applied research utilizing mostly laser spectroscopic methods in the design, development and application of both linear (i.e.
		Experiments are carried out to advance understanding of reaction mechanisms and chemical dynamics of molecular species in the gas, liquid and solid states on the femtosecond to nanosecond timescales.
		Specific areas of interest include the decomposition of energetic materials, the chemistry of nitrogen containing flames, gas phase photochemistry, carrier dynamics in novel semiconductor materials, and atmospheric and environmentally relevant chemistry, such as kinetics of chlorofluorocarbons and heterogeneous chemistry in aqueous aerosol droplets.
	chemistry.nrl.navy.mil /6110/6111 (126 words)

	Amazon.com: Molecular Dynamics (Theoretical and Computational Chemistry): Books: P.B. Balbuena,J.M. Seminario (Site not responding. Last check: 2007-11-05)
		The latest developments in quantum and classical molecular dynamics, related techniques, and their applications to several fields of science and engineering.
		Molecular simulations include a broad range of methodologies such as Monte Carlo, Brownian dynamics, lattice dynamics, and molecular dynamics (MD).
		Molecular dynamics has finally come of age in the last 10 years.
	www.amazon.com /exec/obidos/tg/detail/-/0444829105?v=glance (874 words)

	Molecular Dynamics (Site not responding. Last check: 2007-11-05)
		Note: Molecular Dynamics simulations are CPU and memory intensive for large numbers of particles.
		Molecular Dynamics is free for non-commercial educational use as outlined in the conditions of use.
		Although it is possible to set k, Boltzmann's constant, to something other than 1 using JavaScript, it is the responsibility of the script author to decide on the appropriate units and to convey these units to the student in the text.
	webphysics.davidson.edu /Applets/Molecular/Intro.html (277 words)

	Molecular Dynamics Cinema
		Dry air is a mixture of gases, primarily nitrogen and oxygen with a small amount of argon.
		Molecular nitrogen is composed of two nitrogen atoms joined by a covalent bond of length 1.09 Å.
		Molecular oxygen is similarly composed of two oxygen atoms with a bond length of 1.21 Å.
	www.ems.psu.edu /~bannon/moledyn.html (730 words)

	Amazon.com: Molecular Dynamics Simulation : Elementary Methods (Wiley Professional): Books: J. M. Haile (Site not responding. Last check: 2007-11-05)
		Written especially for the novice, Molecular Dynamics Simulation demonstrates how molecular dynamics simulations work and how to perform them, focusing on how to devise a model for specific molecules and then how to simulate their movements using a computer.
		Molecular dynamics simulations compute the motions of individual molecules in models of solids, liquids, and gases.
		If you're just getting started in molecular dynamics, especially if it's not really where you wanted to be in the first place, this may be the book for you.
	www.amazon.com /exec/obidos/tg/detail/-/047118439X?v=glance (1307 words)

	Molecular Dynamics (Site not responding. Last check: 2007-11-05)
		It offers simple ways to produce 3D molecular structures on screen, a choice of four molecular mechanics force fields and nine semi-empirical quantum mechanical methods, and a selection of geometry optimization techniques to search for stable structures.
		Molecular Dynamics calculations simulate the behavior of molecules at specified temperatures or energies and can be used in many applications, including:
		Illustrating reaction mechanisms with dynamics trajectories using potential surfaces determined by semi-empirical quantum mechanical calculations.
	www.hyper.com /products/description/MM/hyperchem_info6.html (453 words)

	Molecular dynamics
		M.D. solves Newton's equation of motion using a molecular mechanics force field.
		Molecular dynamics produces a (sample of the) Boltzmann distribution of the system.
		Molecular dynamics (eventually) samples different low energy states separated by free energy barriers.
	hekto.med.unc.edu:8080 /COURSES/154/LECTURES/FreeEnergy/DG.html (469 words)

	Molecular Dynamics (MD) Simulation
		It is generally not used to predict structure from sequence or to model the protein folding pathway.
		MD simulation can fold extended sequences to `global' potential energy minima for very small systems (peptides of length ten, or so, in vacuum), but it is most commonly used to simulate the dynamics of known structures.
		Thus, dynamical properties such as time correlation functions and transport coefficients (e.g., diffusion constants, bulk viscosities) can be calculated from a sufficiently long MD trajectory.
	cmm.info.nih.gov /intro_simulation/node23.html (347 words)

	Molecular Dynamics Simulation
		MD allows us to view how the molecular system evolves through time and to constuct average properties of the system given a long enough simulation.
		Then the molecular dynamics is carried out by first heating the system to the experimental temperature by scaling of the velocities.
		Molecular Dynamics (MD) requires the use of a very small timestep, typically 1 femtosecond, to acheive accurate results.
	www.chem.missouri.edu /wong/theory.html (938 words)

	Car-Parrinello molecular dynamics
		is found by damping the coefficient dynamics, so that kinetic energy is gradually removed and the coefficients eventually freeze in the ground-state configuration.
		Car-Parrinello molecular dynamics (CPMD) is the integration of the fictitious wave function coefficient dynamics with the classical molecular dynamics by a single extended Lagrangian.
		Of course, the dynamics of the nuclei in CPMD has only physical meaning if the electronic structure is close to its instantaneous ground-state at each step of the simulation.
	www.cmm.upenn.edu /~ensing/thesis/node10.html (1885 words)

	[No title]
		Parallel Molecular Dynamics Algorithms for Simulation of Molecular Systems, S. Plimpton and B. Hendrickson, chapter in Parallel Computing in Computational Chemistry, edited by T. Mattson, published by the American Chemical Society, Symposium Series 592, 114-132 (1995).
		LAMMPS is our current production-scale molecular MD code (suitable for molecular or atomic systems).
		Particle-Mesh Ewald and rRESPA for Parallel Molecular Dynamics Simulations, S. Plimpton, R. Pollock, M. Stevens, in Proc of the Eighth SIAM Conference on Parallel Processing for Scientific Computing, Minneapolis, MN, March 1997.
	www.cs.sandia.gov /~sjplimp/md.html (564 words)

	The Fritz Haber Center for Molecular Research
		The primary goal of the center is to support research in molecular dynamics and encourage cooperation between German and Israeli scientists.
		A new MD-based approach is explored to search for candidate crystal structures of molecular solids, corresponding to minima of the enthalpy.
		The approach is based on observation of phase transitions in an artificial periodic system with a small unit cell, and relies on the existence of an optimal energy range for observing freezing to low-lying minima.
	www.fh.huji.ac.il (386 words)

	Cover Pages: Molecular Dynamics [Markup] Language (MoDL)
		MoDL - Molecular Dynamics Language (pronounced as 'model') is a "new XML application for simulation data from molecular dynamics.
		Departmental project report by Ashes Dhanna Ganguly, in Postscript, (June 17, 1999), Thesis Report [DisMaL System] - The report discusses two new applications - an XML application for visualization of Chemical Simulations and Molecular Dynamics on the web; and an XML application framework for managing applications in handheld devices.
		Chapter 3 goes into our major work in Molecular Dynamics Visualization over the Web, the design of the new markup language MoDL, the visualization using VRML, the MoDL to VRML converter, an authoring tool to easily markup simulation data and how to use all these tools.
	www.oasis-open.org /cover/modl.html (765 words)

	MELTING PROTEINS: Long-Range forces in Molecular Dynamics Simulations
		The problem has been molecular dynamics (MD), computations that simulate and predict how molecular structure changes over time.
		MD makes it possible, in effect, for the butterflies to fly; the static molecular structures are starting data for simulations in a cell-like environment where scientists can observe their movements.
		This graphic depicts the molecular structure of a large protein, bovine pancreatic trypsin inhibitor, as determined in particle mesh Ewald simulations by Lee Pedersen and Tom Darden.
	www.psc.edu /science/Darden/Darden.html (608 words)

	Mn-Mz
		The model is obtained via optimization of a molecular probability density function (PDF), which is optimized with the variable target function procedure in Cartesian space employing methods of conjugate gradients and molecular dynamics with simulated annealing.
		A general purpose molecular dynamics simulation program which is sufficiently flexible to be used for a wide range of simulation calculations of atomic, ionic and molecular systems.
		Semi-empirical Hamiltonians are used in the electronic part of the calculation to obtain molecular orbitals and the heat of formation and its derivative with respect to molecular geometry.
	stommel.tamu.edu /~baum/linuxlist/linuxlist/node32.html (11482 words)

	Gallery of Dendrimers
		In the course of this work several dendrimers were and are being studied using molecular builders, visualisation and analysis tools along with the Molecular Mechanics and Molecular Dynamics simulations.
		Molecular dynamics simulations were performed for the Dendrimer Box and the fifth generation poly(propyleneimine) dendrimer (PPI-5) with both four and six bengal rose molecules.
		The research interests of these groups are extremely broad ranging from dendrimer synthesis, to polymer science and materials science to molecular recognition and catalysis to device design and fabrication.
	www.wag.caltech.edu /gallery/gallery_dendrimer.html (333 words)

	CPS Education : VMDL : Overview
		I believe it is the atomic hypothesis (or the atomic fact, or whatever you wish to call it) that all things are made of atoms---little particles that move around in perpetual motion, attracting each other when they are a little distance apart, but repelling upon being squeezed into one another.
		The Virtual Molecular Dynamics Laboratory is a software and curriculum package that enables students to work with research quality molecular dynamics simulations.
		NARST 2003 Symposium Read about VMDL and other molecular modeling and visualization tools designed for science education presented at the National Association of Researchers in Science Teaching (NARST) Annual Meeting in Philadelphia, March 23, 2003.
	cps.bu.edu /education/vmdl/index.html (278 words)

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