John D. Chodera

TL;DR: OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility, which makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community.

TL;DR: The multistate Bennett acceptance ratio estimator (MBAR) as mentioned in this paper is an estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment.

TL;DR: A new estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment is presented, which has significant advantages over multiple histogram reweighting methods for combining data from multiple states.

TL;DR: It is shown that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions.

TL;DR: An upper bound for the approximation error made by modeling molecular dynamics with a Markov chain is described and it is shown that this error can be made arbitrarily small with surprisingly little effort.