Richard W. Pastor

TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.

TL;DR: In this paper, a new method for performing molecular dynamics simulations under constant pressure is presented, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphysical "ringing" of the volume associated with the piston mass.

TL;DR: The presented lipid FF is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains and is anticipated to be of utility for simulations of pure lipid systems as well as heterogeneous systems including membrane proteins.

TL;DR: The rate constant for the transition between the equatorial and axial conformations of N‐acetylalanyl‐N′‐methylamide has been determined from Langevin dynamics simulations with no explicit solvent, indicating that both collisional energy transfer with solvent and vibrational energy transfer between internal modes are important in the dynamics of barrier crossing for this system.

TL;DR: The backbone dynamics of Ca(2+)-saturated recombinant Drosophila calmodulin has been studied by 15N longitudinal and transverse relaxation experiments, combined with 15N(1H) NOE measurements, showing a high degree of mobility near the middle of the central helix and anisotropy observed in the motion of the two globular cal modulin domains is much smaller than expected.