Replica exchange Monte Carlo

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

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. 

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... 

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] ... 

Fig. I. Schematic illustration of the implementation of the hyperparallel Monte Carlo method. Each box represents a distinct replica of the simulated system these replicas are simulated simultaneously in a single run. In addition to traditional Monte Carlo trial moves, these replicas can (1) change their state variables in the expanded dimension and (2) exchange configurations with each other, thereby visiting different values of T and fi.

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)... 

---