Electrostatic free energy calculations using the generalized solvent boundary potential method

Generalized solvent boundary potential for computer simulations

Free energy calculations: an efficient adaptive biasing potential method.

We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is computed directly from the population along the coordinates of the free energy. Because of the mollifier, the bias potential is "nonlocal", and its gradient ad...

Electrostatic free energy and its variations in implicit solvent models.

A mean-field approach to the electrostatics for solutes in electrolyte solution is revisited and rigorously justified. In this approach, an electrostatic free energy functional is constructed that depends solely on the local ionic concentrations. The unique set of such concentrations that minimize this free energy are given by the usual Boltzmann distributions through the electrostatic potentia...

Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms

We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replicaexchange method; the latter is also referred to as parallel tempering. We present a new generalized-ensemble algorithm that combines the merits of the two methods; it is referred to as the replica-exchange multicanonical alg...

The Weighted Histogram Analysis Method for Free-Energy Calculations

The Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg and Swendsen’s Multiple Histogram Technique, has been applied for the first time on complex biomolecular Hamiltonians. The method is presented here as an extension of the Umbrella Sampling method for free-energy and Potential of Mean Force calculations. This algorithm possesses the following advantages over methods that a...