49 citations · 157 across the 11 of their papers we have counts for
12 papers
LiveCoMS Roundtable: Discussing Markov state models after two decades of development v1.0
Daniel M. Zuckerman, Gregory R. Bowman, Amedeo Caflisch +14
Markov state models (MSMs) play a central role in the analysis of molecular dynamics (MD) simulations for biomolecules, and MSM methodologies have been under continual development…
Girsanov reweighting for simulations of underdamped Langevin dynamics. Theory
Stefanie Kieninger, Simon Ghysbrecht, Bettina G. Keller
The critical step in a molecular process is often a rare-event and has to be simulated by an enhanced sampling protocol. Recovering accurate dynamical estimates from such biased si…
Clustering -- Basic concepts and methods
Jan-Oliver Felix Kapp-Joswig, Bettina G. Keller
We review clustering as an analysis tool and the underlying concepts from an introductory perspective. What is clustering and how can clusterings be realised programmatically? How…
Grid-based state space exploration for molecular binding
Hana Zupan, Frederick Heinz, Bettina G. Keller
Binding processes are difficult to sample with molecular-dynamics (MD) simulations. In particular, the state space exploration is often incomplete. Evaluating the molecular interac…
A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models
Luca Donati, Marcus Weber, Bettina G. Keller
Dynamical reweighting methods permit to estimate kinetic observables of a stochastic process governed by a target potential from trajectories that have been generate…
Force field optimization by imposing kinetic constraints with path reweighting
P. G. Bolhuis, Z. F. Brotzakis, B. G. Keller
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties…