7 citations · 10 across the 4 of their papers we have counts for
5 papers
Efficient use of non-equilibrium measurement to estimate free energy differences for molecular systems
F. Marty Ytreberg, Daniel M. Zuckerman
A promising method for calculating free energy differences Delta F is to generate non-equilibrium data via ``fast-growth'' simulations or experiments -- and then use Jarzynski's eq…
Unbiased simulation of structural transitions in calmodulin
Daniel M. Zuckerman
We introduce an approach for performing "very long" computer simulations of the dynamics of simplified, folded proteins. Using an alpha-carbon protein model and a fine grid to mimi…
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…
Extrapolative Analysis of Fast-Switching Free Energy Estimates in a Molecular System
Daniel M. Zuckerman, Thomas B. Woolf
We perform an extrapolative analysis of "fast-growth" free-energy-difference (DF) estimates of a computer-modeled, fully-solvated ethane<->methanol transformation. The results sugg…