Jane R. Allison

TL;DR: This overview should help the reader to determine how realistic a coarse-grained model of a biomolecular system is, i.e. whether it reflects the underlying physical mechanisms or merely provides a set of pretty pictures of the process or substances of interest.

TL;DR: The findings indicate that the procedure provides an accurate estimate of the relative statistical weights of the different conformations populated by alpha-synuclein in its natively unfolded state.

TL;DR: These programs are reviewed and the various structural, dynamic, and thermodynamic quantities that can be analyzed using time series, correlation functions, and distributions are described together with technical aspects of their implementation in GROMOS.

TL;DR: The new functionalities that involve modified forces in a molecular dynamics simulation are described: the treatment of electronic polarizability, an implicit surface area and internal volume solvation term to calculate interatomic forces, functions for the GROMOS coarse‐grained supramolecular force field, and nonequilibrium MD to calculate the dielectric permittivity or viscosity.

TL;DR: This work demonstrates that the majority of the tested tools that calculate the order parameters for unsaturated united-atom lipid tails do so incorrectly, and identifies tools that do perform accurate calculations and includes one such program with this work, enabling rapid and accurate calculation of united- atom lipid order parameters.