209 citations · 367 across the 10 of their papers we have counts for
10 papers
Molecular Dynamics simulations and Kelvin Probe Force microscopy to study of cholesterol-induced electrostatic nanodomains in complex lipid mixtures
Elizabeth Drolle, W. F. D. Bennett, K. Hammond +3
The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potent…
Annealed importance sampling of dileucine peptide
Edward Lyman, Daniel M. Zuckerman
Annealed importance sampling is a means to assign equilibrium weights to a nonequilibrium sample that was generated by a simulated annealing protocol. The weights may then be used…
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…