Monte replica-exchange

Kofke, D.A., On the acceptance probability of replica-exchange Monte Carlo trials, J. Chem. Phys. 2002,117, 6911-6914... 

In the original implementation of the replica-exchange method (REM) [67-69], Monte Carlo algorithm was used, and only the coordinates q (and the potential energy function E(q)) had to be taken into account. In molecular dynamics algorithm, on the other hand, we also have to deal with the momenta p. We proposed the following momentum assignment in (4.45) (and in (4.46)) [77] ... 

An alternative to these extended ensembles for the simulation of frustrated magnets is the parallel tempering or replica exchange Monte Carlo method [22-25], Instead of performing a single simulation at a fixed temperature, simulations are performed for M replicas at a set of temperatures Ti,T2,. .., Tm- In addition to standard Monte Carlo updates at a fixed temperature, exchange moves are proposed to swap two replicas between adjacent temperatures. These swaps are accepted with a probability... 

NMR residual dipolar couplings (RDCs), in the form of the projection angles between the respective internuclear bond vectors, have been used by Haliloglu et as structural restraints in the ab initio structure prediction of a test set of six proteins. The restraints have been applied using a recently developed SICHO (5/de CHain Only) lattice protein model that employs a replica exchange Monte Carlo algorithm to search conformational space. The proteins studied were ACP (77 residues), rubredoxin (53 residues), NSl, a 73 residue RNA binding/dimeriz-ation domain, Nodf (35 residues), Crd (137 residues) and Bret domain with 92 residues. 

Monte Carlo with Replica Exchange (p. 375) normal modes (p. 355) rovibrational spectrum (p. 340) simulated annealing (p. 370) spatial cmelation (p. 366) thermalizatiim (p. 367) thermodynamic minimum (p. 353) time correlation (p. 366) torsional potmtial (p. 349)... 

As discussed in Section II. D, the replica exchange Monte Carlo method appears to be an efficient tool for searching the conformational space of reduced protein... 

Thermodynamic Integration Versus Expanded Ensemble and Replica-Exchange Monte Carlo Simulation... 

Within each interval, we use an expanded ensemble technique to explore the sampling points and configurations between neighboring intervals are swapped via replica-exchange Monte Carlo moves [118]. The partition fimction, takes the form ... 

Nanias M et al (2005) Protein structure prediction with the UNRES fOTce-field using replica-exchange Monte Carlo-with-minimization comparison with MCM, CSA, and CFMC. J Comput Chem 26 1472-1486... 

Replica-exchange Monte Carlo method Parallel tempering... 

An important exception are atomic simulations of proteins in explicit solvent, where individual particles (e,g, water molecules) represent the solvent Monte Carlo updates of the system would too frequently collide with solvent particles which causes unacceptably high rejection rates of trial moves. In this case, the cooperative many-body motion is more efficiently simulated by integrating the equations of motion of each particle step by step. It can even be most efficient to combine Monte Carlo and nwlecular dynamics. The most prominent hybrid method is replica-exchange molecular dynamics (REMD), where Langevin simulations ran in different threads at various temperatures and the replicas are exchanged after some time steps with the exchange transition probability (4.92), which effectively is a Monte Carlo step. 

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