A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation [J. Chem. Theory Comput. 2, 1200-1202 (2006)].

A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation

Influence of glycosidic linkage neighbors on disaccharide conformation in vacuum.

Correct description of the free energy of conformation change of disaccharides is important in understanding a variety of biochemical processes and, ultimately, in the manufacture of better food and paper products. In this study, we determine the relative free energy of a series of 12 disaccharides in vacuum using replica exchange molecular dynamics (repMD) simulations. The chosen sugars and th...

Serial Generalized Ensemble Simulations of Biomolecules with Self-Consistent Determination of Weights.

Serial generalized ensemble simulations, such as simulated tempering, enhance phase space sampling through non-Boltzmann weighting protocols. The most critical aspect of these methods with respect to the popular replica exchange schemes is the difficulty in determining the weight factors which enter the criterion for accepting replica transitions between different ensembles. Recently, a method,...

Simulated tempering distributed replica sampling: A practical guide to enhanced conformational sampling

Simulated tempering distributed replica sampling (STDR) is a generalized-ensemble method designed specifically for simulations of large molecular systems on shared and heterogeneous computing platforms [Rauscher, Neale and Pomès (2009) J. Chem. Theor. Comput. 5, 2640]. The STDR algorithm consists of an alternation of two steps: (1) a short molecular dynamics (MD) simulation; and (2) a stochasti...

Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

We present a new type of the Hamiltonian replica-exchange method, where the van der Waals radius parameter and not the temperature is exchanged. By decreasing the van der Waals radii, which control spatial sizes of atoms, this Hamiltonian replica-exchange method overcomes the steric restrictions and energy barriers. Furthermore, the simulation based on this method escapes from the local-minimum...