Modified replica exchange simulation methods for local structure refinement

Article Abstract:

Partial replica exchange molecular dynamics (PREMD) and local replica exchange molecular dynamics (LREMD) is demonstrated as a powerful tool to optimize, simple equilibrium thermodynamic quantities, and to estimate pathways that could be sampled in nonequilibrium simulations. An important assumption used in both the modified REMD methods is that the conformation of majority of the system is insensitive to the smaller region of interest to which replica exchange is applied.

Thermodynamics, Electric fields

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Coupling of replica exchange simulations to a non-Boltzmann structure reservoir

Article Abstract:

Replica exchange molecular dynamics (REMD) simulations are coupled to a reservoir with an arbitrary known probability distribution, while still efficiently driving the REMD replicas toward Boltzmann-weighted ensembles. A cluster based approach is employed to reservoir generation and it is expected that this procedure will extend the range of problems that are amenable to study through REMD simulation.

Analysis, Biomolecules, Transport theory, Mechanical properties

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Improved conformational sampling through an efficient combination of mean-field simulation approaches

Article Abstract:

It is shown for the first time that the GB model can be used to provide a proper implicit solvation treatment for a simulation employing locally enhanced sampling. It is observed that a single LES simulation can provide multiple (and qualitatively different) instances of key transitions.

Simulation methods, Simulation, Solution (Chemistry), Solutions (Chemistry)

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