
	Where results make sense

Topic: Parallel tempering

Related Topics

Monte Carlo method

	Zefsa II: Download sources
		Parallel tempering is able to solve all of the known zeolite materials.
		In parallel tempering, serveral systems are simulated at different, constant temperates, and configurations are ocasionally swapped between systems at adjacent temperatures.
		Parallel tempering is an exact statistical mechanics method, whereas simulated annealing is an approximate method.
	www.mwdeem.rice.edu /zefsaII/instructions.html (3741 words)

	Parallel tempering - Wikipedia, the free encyclopedia
		Parallel tempering, also known as replica exchange, is a simulation method aimed at improving the dynamic properties of Monte Carlo method simulations of physical systems, and of Markov chain Monte Carlo sampling methods more generally.
		This can be ensured by appropriately choosing regular Monte Carlo updates or Parallel Tempering updates with probabilities that are independent of the configurations of the two systems or of the Monte Carlo step.
		The parallel tempering method can be used as a super simulated annealing that does not need restart, since a system at high temperature can feed new local optimizers to a system at low temperature, allowing tunneling between metastable states and improving convergence to a global optimum.
	en.wikipedia.org /wiki/Parallel_tempering (527 words)

	[No title]
		Parallel Tempering (Replica Exchange Method) Parallel tempering, or Replica Exchange Method (REM), was first developed for spin glasses and spread to the protein folding field in the late 1990’s [].
		Cool walking is developed from a combination of aspects of smart-walking, smart darting, and parallel tempering (which are all descendants of jump-walking) and tested on the one-dimensional random potential.
		Describes the parallel tempering algorithm and applies it to Met-enkephalin, a five-residue peptide that is commonly used as a benchmark for simulation.
	socrates.berkeley.edu /~kts/classes/mcb211/multiensemble.doc (2667 words)

	Temperature-Dependent Thermal and Elastic Properties of the Interlamellar Phase of Semicrystalline Polyethylene by ... (Site not responding. Last check: 2007-10-12)
		Parallel tempering between 350 and 450 K was used to simulate several isochoric/isothermal ensembles simultaneously and efficiently, from which the heat capacity, thermal expansion coefficients, Grüneisen coefficients, and the elastic stiffness tensor were determined at atmospheric pressure.
		The coefficient of linear thermal expansion perpendicular to the crystal surface is similar to that of the bulk amorphous melt, whereas the coefficients parallel to the crystal surface mimic those of the crystal phase.
		The interlamellar phase is found to be under tension in the direction perpendicular to the lamellae and in compression in the plane of the crystal surface and parallel to the b-direction of the unit cell (the y-direction of the simulation cell).
	pubs.acs.org /cgi-bin/sample.cgi/mamobx/2006/39/i01/html/ma0518961.html (6639 words)

	Parallel Tempering: Theory, Applications, and New Perspectives
		Parallel tempering is easy to implement, increases the efficiency of computer simulations in almost all the areas it can be applied, and works well on large clusters of CPUs that are becoming more and more widespread.
		We expect that parallel tempering will become a staple method in the computer simulation of complex systems, due to its effectiveness and the ease with which the method can be combined with Monte Carlo or molecular dynamics programs.
		A practical issue is how to use the increase sampling efficiency that parallel tempering brings to improve current force fields, especially implicit solvent models.
	www.rsc.org /Publishing/Journals/CP/News/Deem.asp (373 words)

	Erik Allen's Homepage (Site not responding. Last check: 2007-10-12)
		However, the implementation of a parallel pMC is not an embarassingly parallel problem.
		The main hitch is that the majority of simulation time is devoted to equilibration of the system, which requires a "serial" path through the phase space.
		The main challenge of this project is in the data transfer - the code is currently written in C++ with a large number of classes that are linked by pointer.
	web.mit.edu /ecallen/www (584 words)

	* Inside online - Edition Autumn 2005 *
		Only with the use of massively parallel computers (such as JUMP and the new BlueGene in Jülich) and the development of advanced simulation techniques are we approaching a point where atomistic simulations of stable domains in proteins (usually of order 50 - 200 residues) become feasible.
		Sampling in generalized ensembles, parallel tempering and energy landscape paving are some of the novel algorithms that allow exploring low-energy configurations without the simulations getting trapped in a local minimum.
		Especially interesting for parallel computing is parallel tempering where one distributes on the nodes of a multiprocessor machine N copies of the molecule, each at a different temperature.
	inside.hlrs.de /htm/Edition_02_05/article_02.htm (694 words)

	Parallel Excluded Volume Tempering for Polymer Melts (Site not responding. Last check: 2007-10-12)
		We have developed a technique to accelerate the acquisition of effectively uncorrelated configurations for off-lattice models of dense polymer melts which makes use of both parallel tempering and large scale Monte Carlo moves.
		The method is based upon simulating a set of systems in parallel, each of which has a slightly different repulsive core potential, such that a thermodynamic path from full excluded volume to an ideal gas of random walks is generated.
		Compared to pure stochastic dynamics, this results in an increased efficiency even for a system of chains as short as N = 60 monomers, however at this chain length the large scale Monte Carlo moves were ineffective.
	www.mpip-mainz.mpg.de /~duenweg/Public/parallel_tempering_abstr.html (196 words)

	Protein Structure Prediction Project
		We overcame this obvious shortcoming of the original parallel tempering method with the introduction of an adaptive temperature control for all simulations: Starting with an initial, ordered set of geometrically distributed temperatures we monitored the exchange rate between adjacent temperatures.
		In this work, this acceleration was achieved by the use of a modified version of the parallel tempering approach.
		The three-helix HIV accessory protein is among the largest proteins predictably folded to date, the introduction of the modified parallel tempering method is thus an important step towards the development of parallel optimization techniques that can be efficiently implemented on massively parallel, distributed computational architectures that dominate the high-end of presently available computational resources.
	iwrwww1.fzk.de /biostruct/PSP/1f4ipt.htm (2343 words)

	Research Projects on the Helix Systems (Site not responding. Last check: 2007-10-12)
		The assembly of a parallel β-sheet from the amorphous state mainly occurs via a bottleneck channel where the inter-strand Asn - Asn stacking is the major interaction.
		REMD are run in parallel at a series of temperatures spanning from low temperature (usually at 270K) to high temperature (600-1000K, depending on the number of CPUs available).
		In contrast to the stabilization from electrostatic interactions, the pi-stacking is also shown to stabilize the parallel beta-strands.
	helix.nih.gov /research/tsaih.html (886 words)

	Feedback-optimized parallel tempering Monte Carlo
		We introduce an algorithm for systematically improving the efficiency of parallel tempering Monte Carlo simulations by optimizing the simulated temperature set.
		Conventionally, a temperature set is chosen in such a way that the acceptance rates for replica swaps between adjacent temperatures are independent of the temperature and large enough to ensure frequent swaps.
		We illustrate the feedback-optimized parallel tempering algorithm by studying the two-dimensional Ising ferromagnet and the two-dimensional fully frustrated Ising model, and briefly discuss possible feedback schemes for systems that require configurational averages, such as spin glasses.
	repositories.cdlib.org /postprints/1436 (253 words)

	Zefsa II: Description
		In the most difficult cases, the superior method of parallel tempering rather than simulated annealing is necessary.
		Roughly 10% of the known zeolites require the method of parallel tempering.
		The parallel tempering option is no more difficult to use than is the simulated annealing.
	sdpd.univ-lemans.fr /DU-SDPD/nexus/zefsa/descript.htm (630 words)

	[No title] (Site not responding. Last check: 2007-10-12)
		The Parallel Tempering Monte Carlo (PTMC) method has been found to be an effective approach for reducing quasiergodicity in Monte Carlo (MC) simulations (see e.g., F. Calvo et al., J. Chem.
		The PTMC procedure is ideally suited for parallel computing environments, as the simulations at the N temperatures can be carried out on N different processors.
		Kenneth Jordan using Fortran 90 and is parallelized using MPI calls.
	www.pitt.edu /~alfonso/PARALLEL_TEMPERING/pt.html (2080 words)

	Using novel variable transformations to enhance conformational sampling in molecular dynamics
		Parallel tempering methods introduce a series of M simulations at different temperatures which are permitted to interchange.
		Moreover, the new approach could be combined with complementary transformations [] that help overcome entropic barriers as well as employed to enhance the efficiency of other techniques such as parallel tempering.
		The new technique can easily be combined with complementary transformations [] that help overcome entropic barriers as well as with parallel tempering schemes.
	homepages.nyu.edu /~mt33/eccc8/var_trans/PRL_vtrans_eccc8.html (1988 words)

	Graduate Chemical Engineering Seminar Series (Site not responding. Last check: 2007-10-12)
		Backbone atoms are equilibrated with a biased rebridging scheme, and side-chain atoms are equilibrated with a look-ahead configurational bias Monte Carlo.
		Parallel tempering is shown to be an essential component of the method.
		The approach is illustrated on a variety of proline-containing cyclic peptides that undergo cis/trans isomerization of the CONH amide bond.
	unr.edu /homepage/vvasquez/seminar/deem.html (329 words)

	parallel simulation techniques (Site not responding. Last check: 2007-10-12)
		We have recently developed new computer codes which allow molecular dynamics and Monte Carlo simulations to be carried out in parallel.
		These techniques are readily translated to other parallel systems, paving the way for a new generation of large-scale simulations of chemical systems.
		Parallel computer simulation techniques for the study of macromolecules Wilson M. R., Ilnytskyi J. in Computer Simulations of liquid crystals and polymers, eds Pasini P., Zannoni C. and Zŭmer S., (Kluwer 2004), 335-356.
	www.dur.ac.uk /mark.wilson/parallel.html (289 words)

	FAQ - FOX, Free Objects for Crystallography Wiki
		The advantage of such an approach is that if the modelization (parametrization) of some objects changes, the algorithms do not need any modification since they use a generic approach to the objects.
		The algorithm is invariant with time and therefore does not require from the user to choose the number of trial and the temperature schedule.
		In other words, always use Parallel Tempering, unless you are interested in algorithms and want to play with SA.
	objcryst.sourceforge.net /Fox/FAQ (2136 words)

	FreeScience - Books - Monte Carlo
		From its origins in data analysis, the parallel tempering method has become a standard workhorse of physiochemical simulations.
		We mention a selected set of the many applications that have become possible with the introduction of parallel tempering and we suggest several promising avenues for future research.
		After briefly sketching the history of multicanonical calculations and their range of application, a general introduction in the context of the statistical physics of the d-dimensional generalized Potts models is given.
	www.freescience.info /books.php?id=33 (746 words)

	Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: ... (Site not responding. Last check: 2007-10-12)
		the stability and population of the DFAKF parallel
		with temperature, indicating a steady decrease of parallel
		0.75 is the closest one near the in-register parallel
	www.pnas.org /cgi/content/full/102/23/8174 (3666 words)

	Accelrys
		The indexing of the powder pattern is followed by the determination of the space group and the refinement of the cell parameters, peak shape and background parameters by a modified Pawley method.
		Then, a global optimization algorithm, either Monte Carlo Simulating Annealing or parallel tempering, is used to generate trial structures in direct space finding the solution that maximizes the agreement between the simulated and experimental powder diffraction pattern.
		The SA search was trapped in a deep local minimum but the parallel tempering algorithm found the global minimum in 214503 steps
	www.accelrys.com /reference/cases/studies/an_inorganics.html (918 words)

	vsevcosmos: Searching for Globally Optimal Functional Forms for Inter-Atomic Potentials Using Parallel Tempering
		We develop a Genetic Programming-based methodology that enables discovery of novel functional forms for classical inter-atomic force-fields, used in molecular dynamics simulations.
		We performed an automatic functional form fitting procedure starting with a population of random functions, using a genetic programming functional formulation, and a parallel tempering Metropolis-based optimization algorithm.
		We also find that our parallel tempering Metropolis-based approach significantly improves the optimization convergence time, and takes good advantage of the parallel cluster architecture.
	vsevcosmos.livejournal.com /19731884.html (259 words)

	Appendix A: The Lanczós algorithm (Site not responding. Last check: 2007-10-12)
		Next: Appendix B: Parallel tempering Up: Sampling activated mechanisms in Previous: Acknowledgement
		The Lanczós algorithm [23] provides an efficient way to extract a limited spectrum of eigenvalues and eigenvectors for a high-dimensional problem without requiring the evaluation and diagonalization of the full
		This is especially so because we can make use of the eigendirection used in the previous iteration as a seed for the new recursion.
	www.phy.ohiou.edu /~malek/protein7/node14.html (256 words)

	Session N19 - Computer Simulations of Polymers I.
		The standard parallel tempering technique is applied to a dense bead-spring polymer melt.
		As a tempering parameter we use directly the strength of the excluded volume interaction, thus facilitating the use of pivot moves in the weak-interaction limit.
		We have used recently developed parallel tempering (PT) technique for molecular dynamics (MD) simulations of Polybutadiene (PBD) melts.
	flux.aps.org /meetings/YR01/MAR01/abs/S5190.html (2323 words)

	Predicting the Signaling State of Photoactive Yellow Protein -- Vreede et al. 88 (5): 3525 -- Biophysical Journal (Site not responding. Last check: 2007-10-12)
		parallel tempering runs were continued for on average 8–10ns,
		The free energy diagrams for the chromophore binding pocket are plotted for each nanosecond of the parallel tempering simulation starting from a protonated cis-chromophore (Kort et al., 2004
		We should stress that the parallel tempering simulations, although
	www.biophysj.org /cgi/content/full/88/5/3525 (6038 words)

	Research: Gustavo E. López, Ph.D.
		These models are based on classical and quantum mechanical formalisms, i.e.
		path integral and parallel tempering Monte Carlo on various ensembles.
		Some of the systems that are being considered are atomic and molecular nanostructures, polymeric materials, bulk and confined fluids, model peptides, and Langmuir monolayers.
	www.uprm.edu /wquim/research_facu/lopez.html (215 words)

	Session Z14 - General: Polymers, Biopolymers, Complex Systems.
		[Z14.012] Hyper-Parallel Tempering Monte Carlo Method and It's Applications
		A new generalized hyper-parallel tempering Monte Carlo molecular simulation method is presented for study of complex fluids.
		The method is particularly useful for simulation of many-molecule complex systems, where rough energy landscapes and inherently long characteristic relaxation times can pose formidable obstacles to effective sampling of relevant regions of configuration space.
	flux.aps.org /meetings/YR00/MAR00/abs/S9330.html (2291 words)

	The Stability and Dynamics of the Human Calcitonin Amyloid Peptide DFNKF -- Tsai et al. 87 (1): 146 -- Biophysical ... (Site not responding. Last check: 2007-10-12)
		comparative MD studies have found that the parallel ß-stranded
		we probe the stability and dynamics of the small parallel DFNKF
		process of parallel ß-sheet formation from the out-of-register
	www.biophysj.org /cgi/content/abstract/87/1/146 (379 words)

Try your search on: Qwika (all wikis)