David S. Cerutti

TL;DR: Together, the improvements made to both the small molecule and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field.

TL;DR: Progress is reported in graphics processing unit (GPU)-accelerated molecular dynamics and free energy methods in Amber, including free energy perturbation and thermodynamic integration methods with support for nonlinear soft-core potential and parameter interpolation transformation pathways.

TL;DR: The AMBER ff15ipq force field for proteins is the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent, and reproduces penta-alanine J-coupling constants exceptionally well.

TL;DR: An old technique for improving the accuracy of mesh-based field calculations is drawn on to extend the popular Smooth Particle Mesh Ewald algorithm as the StaggeredMesh Ewald (StME) algorithm, which improves the accuracies of computed forces and reduces the drift in system momentum inherent in the SPME method by averaging the results of two separate reciprocal space calculations.

TL;DR: The IPolQ method for fitting nonpolarizable point charges to implicitly represent the energy of polarization for systems in pure water is developed and is general and applicable to arbitrary solutes.