Probability distributions for complex systems: adaptive umbrella sampling of the potential energy

Article Abstract:

The adaptive umbrella sampling method is extended through the introduction of a molecular dynamics algorithm based on potential energy. This proposed adaptive umbrella sampling technique, which is recommended for expediting the simulation time for generating equilibrium features of molecular systems, offers a general sampling method for obtaining distributions for several degrees of freedom. This was made possible through the sampling of the significant local minima and the transition states while avoiding to accumulate excessive, irrelevant conformations.

Conformational analysis, Statistical sampling, Sampling (Statistics), Chemical equilibrium

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Absolute binding free energies: A quantitative approach for their calculation

Article Abstract:

The computation of absolute binding affinities by molecular dynamics (MD) based free energy simulations is analyzed, and an exact method to carry out such a computation is presented. Although the techniques were originally developed for the gas phase, the resulting expression is exact, since all contributions from solute-solvent interactions cancel from the final result.

Binding energy

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Folding time distributions as an approach to protein folding kinetics

Article Abstract:

A 27-residue lattice heteropolymer subject to Monte Carlo dynamics on a simple cubic lattice is studied over a range of temperatures. It is shown that the calculated folding kinetics can be modeled by a system of kinetic equations with the essential rate constants determined from the Monte Carlo simulations and the resulting folding time distributions.

Polymers, Monte Carlo method, Monte Carlo methods, Dynamics, Dynamics (Mechanics)

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