Dynamical reweighting for biased rare event simulations
BG Keller, PG Bolhuis - Annual Review of Physical Chemistry, 2024 - annualreviews.org
Dynamical reweighting techniques aim to recover the correct molecular dynamics from a
simulation at a modified potential energy surface. They are important for unbiasing …
simulation at a modified potential energy surface. They are important for unbiasing …
A review of Girsanov reweighting and of square root approximation for building molecular Markov state models
Dynamical reweighting methods permit to estimate kinetic observables of a stochastic
process governed by a target potential V ̃ (x) from trajectories that have been generated at a …
process governed by a target potential V ̃ (x) from trajectories that have been generated at a …
Overcoming the timescale barrier in molecular dynamics: Transfer operators, variational principles and machine learning
One of the main challenges in molecular dynamics is overcoming the 'timescale barrier': in
many realistic molecular systems, biologically important rare transitions occur on timescales …
many realistic molecular systems, biologically important rare transitions occur on timescales …
Reweighted manifold learning of collective variables from enhanced sampling simulations
Enhanced sampling methods are indispensable in computational chemistry and physics,
where atomistic simulations cannot exhaustively sample the high-dimensional configuration …
where atomistic simulations cannot exhaustively sample the high-dimensional configuration …
Dynamical reweighting methods for Markov models
Highlights•Advances, limitations and applications of dynamical reweighting for Molecular
Dynamics simulations.•Classification of dynamical reweighting methods.•Enhanced …
Dynamics simulations.•Classification of dynamical reweighting methods.•Enhanced …
[HTML][HTML] Path probability ratios for Langevin dynamics—Exact and approximate
S Kieninger, BG Keller - The Journal of Chemical Physics, 2021 - pubs.aip.org
Path reweighting is a principally exact method to estimate dynamic properties from biased
simulations—provided that the path probability ratio matches the stochastic integrator used …
simulations—provided that the path probability ratio matches the stochastic integrator used …
Convergences of the squareroot approximation scheme to the Fokker–Planck operator
M Heida - Mathematical Models and Methods in Applied …, 2018 - World Scientific
We study the qualitative convergence behavior of a novel FV-discretization scheme of the
Fokker–Planck equation, the squareroot approximation scheme (SQRA), that recently was …
Fokker–Planck equation, the squareroot approximation scheme (SQRA), that recently was …
Markov models from the square root approximation of the Fokker–Planck equation: Calculating the grid-dependent flux
Molecular dynamics (MD) are extremely complex, yet understanding the slow components of
their dynamics is essential to understanding their macroscopic properties. To achieve this …
their dynamics is essential to understanding their macroscopic properties. To achieve this …
Consistency and convergence for a family of finite volume discretizations of the Fokker–Planck operator
We introduce a family of various finite volume discretization schemes for the Fokker–Planck
operator, which are characterized by different Stolarsky weight functions on the edges. This …
operator, which are characterized by different Stolarsky weight functions on the edges. This …
The Kramers turnover in terms of a macro-state projection on phase space
We have investigated how Langevin dynamics is affected by the friction coefficient using the
novel algorithm ISOKANN, which combines the transfer operator approach with modern …
novel algorithm ISOKANN, which combines the transfer operator approach with modern …