152 citations · 157 across the 7 of their papers we have counts for
4 papers · 1 filter
Reducing the Bias and Uncertainty of Free Energy Estimates by Using Regression to Fit Thermodynamic Integration Data
Conrad Shyu, F. Marty Ytreberg
This report presents the application of polynomial regression for estimating free energy differences using thermodynamic integration. We employ linear regression to construct a pol…
A "black-box" re-weighting analysis can correct flawed simulation data, after the fact
F. Marty Ytreberg, Daniel M. Zuckerman
There is a great need for improved statistical sampling in a range of physical, chemical and biological systems. Even simulations based on correct algorithms suffer from statistica…
Single-ensemble nonequilibrium path-sampling estimates of free energy differences
F. Marty Ytreberg, Daniel M. Zuckerman
We introduce a straightforward, single-ensemble, path sampling approach to calculate free energy differences based on Jarzynski's relation. For a two-dimensional ``toy'' test syste…
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…