24 citations · 26 across the 4 of their papers we have counts for
Showing 2006 · physics.bio-phShow all
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physics.bio-ph2006
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…
physics.bio-ph2006
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…
physics.bio-ph2006
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…