24 citations · 48 across the 15 of their papers we have counts for
5 papers · 1 filter
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…
The structural de-correlation time: A robust statistical measure of convergence of biomolecular simulations
Edward Lyman, Daniel M. Zuckerman
Although atomistic simulations of proteins and other biological systems are approaching microsecond timescales, the quality of trajectories has remained difficult to assess. Such a…
A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation
Daniel M. Zuckerman, Edward Lyman
Because of growing interest in temperature-based sampling methods like replica exchange, this note aims to make some observations and raise some potentially important questions whi…
Ensemble based convergence assessment of biomolecular trajectories
Edward Lyman, Daniel M. Zuckerman
Assessing the convergence of a biomolecular simulation is an essential part of any computational investigation. This is because many important quantities (e.g., free energy differe…
Resolution exchange simulation with incremental coarsening
Edward Lyman, Daniel M. Zuckerman
We previously developed an algorithm, called resolution exchange, which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-reso…