Replica-exchange molecular dynamics

Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314 141—151. 

Molecular dynamics has also been used to replace the MC moves for conformational advancement [43]. In the molecular dynamics version of parallel tempering, often referred to as replica exchange molecular dynamics, momenta are used in the propagation scheme such that a constant temperature is maintained between the swaps. After the swap in conformational space (with the same acceptance criterion as in the MC implementation), a readjustment in momentum space is also needed. This is done by renewing the momenta for replica i by the transformation... 

Sanbonmatsu, K. Y. Garcia, A. E., Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics, Prot. Struct. Function Genetics Feb 2002, 46, 225-234. 

Rhee, Y. M. Pande, V. S., Multiplexed-replica exchange molecular dynamics method for protein folding simulation, Biophys. J. 2003, 84, 775-786. 

Nymeyer, H. How efficient is replica exchange molecular dynamics An analytic approach. J. Chem. Theory Comput. 2008, 4, 626-36. 

Nguyen, P.H., Mu, Y., and Stock, G. (2005) Structure and energy landscape of a photoswitchable peptide A replica exchange molecular dynamics study. Proteins 60, 485 194. 

Abstract We present replica exchange molecular dynamics calculations of the conformational space... 

We applied replica exchange molecular dynamics (REMD) calculations for conformational sampling of the AD in explicit water, where the AD is treated quantum mechanically and the water molecules classically, using the TIP3P [29] model. For comparison purposes, the same calculation is done where the AD is treated by a classical force field, using our recently developed AMBER ff99SB [30] parameters. 

Replica Exchange Molecular Dynamics of Alanine Dipeptide in Explicit Water... 

This chapter highlighted the use of replica exchange molecular dynamics calculations for the investigation of the performance of the PM3, PDDG/PM3 and PM3PC Hamiltonians as applied for the conformational equilibrium of alanine dipeptide in the gas phase and water solution, a convenient model system for the study of biological molecules. 

REMD see Replica Exchange Molecular Dynamics renormalized approximations, 6, 83, 92 Replica Exchange Molecular Dynamics, 2, 83, 85, 87, 89-91, 93, 95, 222... 

Baumketner, A., Shea, J.E. The thermodynamics of folding of a beta hairpin peptide probed through replica exchange molecular dynamics simulations. Theor. Chem. Acc. 2006,116,262-73. 

Jiang, W., M. Hodoscek, and B. Roux. 2009. Computation of absolute hydration and binding free energy with free energy perturbation distributed replica-exchange molecular dynamics (FEP/REMD). Journal of Chemical Theory and Computation. 5, 2583. 

In a related paper, Ikeda et al. has presented a combined use of replica-exchange MD and solid-state MAS NMR spectral simulations for determining the structure and orientation of membrane-bound peptide." First, an ensemble of low energy structures of mastoparan-X, a wasp venom peptide, in lipid bilayers was generated by replica exchange molecular dynamics (REMD) simulation with the implicit membrane/solvent model. Next, peptide structures compatible with experimental chemical shifts of C,, Cp and C carbons were selected from the ensemble. Chemical shifts of C, alone were sufficient for the selection with backbone rmsd s of 0.8 A from the experimentally determined structure. The dipolar couplings between the peptide protons and lipid nuclei were obtained from the C-... 

Enhanced Sampling Methods Replica Exchange Molecular Dynamics... 

Particle-based simulation techniques include atomistic MD and coarse-grained molecular dynamics (CG-MD). Accelerated dynamics methods, such as hyperdynamics and replica exchange molecular dynamics (REMD), are very promising for circumventing the timescale problem characteristic of atomistic simulations. Structure and dynamics at the mesoscale level can be described within the framework of coarse-grained particle-based models using such methods as stochastic dynamics (SD), dissipative particle dynamics (DPD), smoothed-particle hydrodynamics (SPH), lattice molecular dynamics (LMD), lattice Boltzmann method (IBM), multiparticle collision dynamics (MPCD), and event-driven molecular dynamics (EDMD), also referred to as collision-driven molecular dynamics or discrete molecular dynamics (DMD). 

---