MOTIVATION Motion is inherent in molecular interactions. Molecular flexibility must be taken into account in order to develop accurate computational techniques for predicting interactions. Energy-based methods currently used in molecular modeling (i.e. molecular dynamics, Monte Carlo algorithms) are, in practice, only able to compute local motions while accounting for molecular flexibility. How...

We review recent molecular modeling efforts to shed light on the mechanisms of zeolite formation. We focus on studies that model the early stages of silica polymerization and zeolite nucleation. Electronic structure calculations, classical molecular dynamics, atomistic Monte Carlo simulations and Monte Carlo simulations of lattice models have been used to probe the formation of zeolites and mes...

Network-based methods provide an accurate description of the free-energy landscape of peptides and proteins sampled by molecular dynamics simulations. To that end, it is necessary to group the individual snapshots in a meaningful way. The inherent structures (ISs) provide an appropriate discretization of the trajectory into microstates, avoiding problems that can arise in clustering algorithms ...

Employing a simple hydrophobic-polar heteropolymer model, we compare thermodynamic quantities obtained from Andersen and Nosé-Hoover molecular dynamics as well as replicaexchange Monte Carlo methods. We find qualitative correspondence in the results, but serious quantitative differences using the Nosé-Hoover chain thermostat. For analyzing the deviations, we study different parameterizations of...