49 citations · 157 across the 11 of their papers we have counts for
5 papers · 1 filter
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…
GROMACS Stochastic Dynamics and BAOAB are equivalent configurational sampling algorithms
Stefanie Kieninger, Bettina G. Keller
Two of the most widely used Langevin integrators for molecular dynamics simulations are the GROMACS Stochastic Dynamics (GSD) integrator and the splitting method BAOAB. In this let…