Fragment molecular orbital−based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion

Recent Advances in Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations

Modeling Nanocomposites for Molecular Dynamics (md) Simulations

Animated molecular dynamics simulations of hydrated caesium-smectite interlayers

Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers) provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs formed inner sphere complexes with the mineral surface, and could be seen to j...

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular cl...

Ion motions in molecular dynamics simulations on DNA.

Counterions play a significant role in DNA structure and function, and molecular dynamics (MD) simulations offer the prospect of detailed description of the dynamical structure of ions at the molecular level. However, the motions of mobile counterions are notably slow to converge in MD on DNA. Obtaining accurate and reliable MD simulations requires knowing just how much sampling is required for...