162 citations · 894 across the 45 of their papers we have counts for
11 papers · 1 filter
Weighted ensemble: Recent mathematical developments
D. Aristoff, J. Copperman, G. Simpson +2
The weighted ensemble (WE) method, an enhanced sampling approach based on periodically replicating and pruning trajectories in a set of parallel simulations, has grown increasingly…
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 (…
Automated sampling assessment for molecular simulations using the effective sample size
Xin Zhang, Divesh Bhatt, Daniel M. Zuckerman
To quantify the progress in development of algorithms and forcefields used in molecular simulations, a method for the assessment of the sampling quality is needed. We propose a gen…
Symmetry of forward and reverse path populations
Divesh Bhatt, Daniel M. Zuckerman
In this note, we address formally the issue of symmetry for probabilities of different dynamical pathways in the forward and reverse directions of a conformational transition. Our…