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One popular approach to incorporating experimental data into molecular simulations is to restrain the ensemble average of observables to their experimental values. Here I derive equations for the equilibrium distributions generated by restrained ensemble simulations and the corresponding expected values of observables. My results suggest a method to restrain simulations so that they generate distributions that are minimally perturbed from the unbiased distributions while reproducing the experimental values of the observables within their measurement uncertainties.
In this work, a new algorithm is proposed to compute single particle (infinite dilution) thermodiffusion using Non-Equilibrium Molecular Dynamics simulations through the estimation of the thermophoretic force that applies on a solute particle. This s
We present a molecular dynamics simulation method for the computation of the solubility of organic crystals in solution. The solubility is calculated based on the equilibrium free energy difference between the solvated solute and its crystallized sta
A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated tempering were per
We demonstrate that selection of the minimal value of ordered variables leads in a natural way to its distribution being given by the Tsallis distribution, the same as that resulting from Tsallis nonextensive statistics. The possible application of t
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had previousl