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Simple synthetic molecular dynamics for efficient trajectory generation
John D. Russo, Daniel M. Zuckerman
Synthetic molecular dynamics (synMD) trajectories from learned generative models have been proposed as a useful addition to the biomolecular simulation toolbox. The computational e…
Unbiased estimation of equilibrium, rates, and committors from Markov state model analysis
John D. Russo, Jeremy Copperman, David Aristoff +2
Markov state models (MSMs) have been broadly adopted for analyzing molecular dynamics trajectories, but the approximate nature of the models that results from coarse-graining into…
Iterative trajectory reweighting for estimation of equilibrium and non-equilibrium observables
John D. Russo, Jeremy Copperman, Daniel M. Zuckerman
We present two algorithms by which a set of short, unbiased trajectories can be iteratively reweighted to obtain various observables. The first algorithm estimates the stationary (…