Replica-exchange molecular dynamics REMD

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. 

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-... 

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). 

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. 

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

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. 

W. Jiang and B. Roux,/. Chem. Theory Comput., 6(9), 2559-2565 (2010). Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. 

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