162 citations · 330 across the 11 of their papers we have counts for
4 papers · 1 filter
Rapid Determination of Multiple Reaction Pathways in Molecular Systems: The Soft-Ratcheting Algorithm
Daniel M. Zuckerman, Thomas B. Woolf
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure,…
Systematic Finite-Sampling Inaccuracy in Free Energy Differences and Other Nonlinear Quantities
Daniel M. Zuckerman, Thomas B. Woolf
Systematic inaccuracy is inherent in any computational estimate of a non-linear average, such as the free energy difference (Delta-F) between two states or systems, because of the…
Dependence of Sidechain Rotamer Preference on Backbone Conformation: Relative Free Energy Calculations for Valine and Leucine
John G. Pearson, Thomas B. Woolf
Three dimensional relative free energy calculations are used to directly calculate the dependence of the preferred sidechain rotamers for valine and leucine on the conformation of…
Theory of Systematic Computational Error in Free Energy Differences
Daniel M. Zuckerman, Thomas B. Woolf
Systematic inaccuracy is inherent in any computational estimate of a non-linear average, due to the availability of only a finite number of data values, N. Free energy differences…