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physics.comp-ph2022
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…
physics.comp-ph2017★ 25 cited
Estimation of the infinitesimal generator by square-root approximation
Luca Donati, Martin Heida, Bettina G. Keller +1
For the analysis of molecular processes, the estimation of time-scales, i.e., transition rates, is very important. Estimating the transition rates between molecular conformations i…