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Physica A, ISSN 0378-4371, 12/2017, Volume 488, pp. 121 - 131
Although the topological Berezinskii–Kosterlitz–Thouless transition was for the first time described by 40 years ago, it is still a matter of discussion. It... 
Wang–Landau replica exchange | XY model | Topological phase transition | Wang-Landau replica exchange | XY-MODEL | VORTICES | PHYSICS, MULTIDISCIPLINARY | KOSTERLITZ-THOULESS TRANSITION | ANTIFERROMAGNET | MONTE-CARLO | TEMPERATURE | SPIN-DYNAMICS | SYSTEMS | HIGH-PRECISION | 2 DIMENSIONS | Anisotropy | Analysis | Models
Journal Article
Carbohydrate polymers, ISSN 0144-8617, 05/2016, Volume 141, pp. 99 - 105
...: the highly advantageous replica exchange molecular dynamics (REMD) simulation (particularly suitable for studies of conformational changes... 
Large-ring cyclodextrin | Conformational changes | Replica exchange molecular dynamics | ε-Cyclodextrin | POLYMER SCIENCE | STABILITY | X-RAY-STRUCTURE | CHEMISTRY, ORGANIC | CDN | BETA | BIOMOLECULAR FORCE-FIELD | CYCLOAMYLOSE | GLYCAM06 | CHEMISTRY, APPLIED | FREE-ENERGY | epsilon-Cyclodextrin | LARGE-RING CYCLODEXTRINS | WATER
Journal Article
The journal of physical chemistry. B, ISSN 1520-6106, 05/2007, Volume 111, Issue 19, pp. 5405 - 5410
Journal Article
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, ISSN 1364-503X, 06/2009, Volume 367, Issue 1897, pp. 2595 - 2606
Journal Article
Concurrency and computation, ISSN 1532-0626, 02/2017, Volume 29, Issue 4, pp. np - n/a
Summary We present Hadoop‐based replica exchange (HaRE), a Hadoop‐based implementation of the replica exchange scheme developed primarily for replica exchange statistical temperature molecular dynamics, an example of a large... 
GENI | replica exchange statistical temperature molecular dynamics (RESTMD) | Hadoop MapReduce | replica exchange | distributed cyberinfrastructure | enhanced conformational sampling | COMPUTER SCIENCE, SOFTWARE ENGINEERING | TOOLKIT | COMPUTER SCIENCE, THEORY & METHODS | MOLECULAR-DYNAMICS SIMULATIONS | MAPREDUCE | Molecular dynamics | Global information infrastructure | Exchanging | Optical communication | Computer simulation | Computation | Exchange | Networks | Dynamical systems
Journal Article
Journal of chemical theory and computation, ISSN 1549-9618, 01/2013, Volume 9, Issue 1, pp. 13 - 17
The method of window exchange umbrella sampling molecular dynamics (WEUSMD) with a preoptimized parameter set was recently used to obtain the most probable conformations and the energetics of transmembrane (TM... 
FREE-ENERGY CALCULATIONS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | MEMBRANE-PROTEIN STRUCTURE | REPLICA-EXCHANGE | DIMERIZATION | MOLECULAR-DYNAMICS SIMULATIONS | ASSOCIATION | ALPHA-HELICES | INSIGHTS | Glycophorin A | Potential of Mean Force | Replica Exchange Methods | First Passage Time Optimization
Journal Article
Journal of chemical theory and computation, ISSN 1549-9618, 10/2009, Volume 5, Issue 10, pp. 2583 - 2588
... replica is distributed to different nodes of a large cluster [Theor. Chem. Acc. 2003, 109, 140]. Here, we use the framework provided by REPDSTR to combine a staged free energy perturbation protocol with replica-exchange molecular dynamics... 
CHEMISTRY, PHYSICAL | COMPUTER-SIMULATIONS | CHARMM | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | SAMPLING | THERMODYNAMICS | INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY | REPLICAS | CONVERGENCE | SIMULATION | HYDRATION | FREE ENERGY
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 09/2010, Volume 133, Issue 11, pp. 114113 - 114113-8
.... This approach, serial tempering without exchange (STeWiE), has the same performance as serial tempering in the limit that exchanges are frequent, is simpler to implement, and has fewer adjustable parameters than conventional serial tempering. The equivalence of serial tempering and STeWiE also provides a convenient route for estimating and optimizing the performance of serial tempering simulations and other generalized-ensemble methods. 
ENSEMBLE | sampling methods | tempering | solvation | ALGORITHM | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | MONTE-CARLO METHOD | MOLECULAR-DYNAMICS METHODS | HELIX-COIL TRANSITION | REPLICA-EXCHANGE | SIMULATIONS | DENSITY-OF-STATES | FREE-ENERGY | EFFICIENT | Probability | Thermodynamics | Temperature | Monte Carlo Method | Molecular Dynamics Simulation
Journal Article
Journal of physics. Condensed matter, ISSN 1361-648X, 2019, Volume 31, Issue 8, p. 085901
.... This is achieved by harnessing the power of modern-day cluster supercomputers using the replica exchange Monte Carlo method coupled directly with structural relaxation and energy calculation... 
spinel | PHYSICS, CONDENSED MATTER | DESIGN | CLUSTERS | configurational sampling | replica exchange | ALGORITHM | MPI | first-principles simulation | EFFICIENT | PYTHON
Journal Article
Molecular Physics: Proceedings from the 53rd Sanibel Meeting, ISSN 0026-8976, 02/2014, Volume 112, Issue 3-4, pp. 379 - 384
Journal Article