A new local ab initio molecular dynamics method, namely elongation molecular dynamics (ELG-MD) is proposed for highly efficient simulations of aperiodic polymer systems. ELG-MD combines the elongation method (ELG) with the Gear predictor corrector (GPC) algorithm of molecular dynamics simulation. In this method, the local gradients acting on the atom's nucleus in the active region are calculate...

Understanding the distance distribution and dynamics between moieties attached to the walls of a resorcin[4]arene cavitand, which is switchable between an expanded kite and a contracted vase form, might enable the use of this molecular system for the study of fundamental distance-dependent interactions. Toward this goal, a combined experimental and molecular dynamics (MD) simulation study on do...

The dynamics of brittle fracture in vitreous silica has been a subject of many molecular dynamics (MD) simulations and experiments. A striking similarity between both simulations and experiments is the observation of nanoscale voids that eventually coalesce leading to failure. In this work, we review the above MD simulations and carry out further MD investigations using two variations of classi...

In this work, we study the diffusion of nanodroplets on smooth surfaces through molecular dynamics (MD) simulations and theoretical analyses. Molecular dynamics simulations show that nanodroplet surface diffusion is different from that of single molecules and solid particles. The dependence of nanodroplet diffusion coefficient on temperature undergoes a transition from linear to nonlinear as th...

Molecular dynamics (MD) simulation is a well-established method for understanding protein dynamics. Conformations from unrestrained MD simulations have yet to be assessed for blind virtual screening (VS) by docking. This study presents a critical analysis of the predictive power of MD snapshots to this regard, evaluating two well-characterized systems of varying flexibility in ligand-bound and ...

In the past years an increasing number of graphical user interfaces for Molecular Dynamics (MD) were presented and concomitantly, more and more Molecular Dynamics studies were published. With the easier application of MD software packages the field runs the risk however, of being pervaded with unreliable results. Therefore, possible benefits and caveats have to be carefully balanced. Here we ou...

has been a major hurdle on the use of these compensating potentials more generally in constrained MD simulations. Rigid internal constraints are used in molecular models to speed up molecular dynamics (MD) simulations. It is well recognized that This paper analyzes the structure of the compensating statistical averages from such constrained MD simulations differ by potential and its gradient an...

Classical molecular dynamics (MD) has been successfully applied to model radiation-induced dynamics of highly ionized assemblies of atoms, including the dynamics of electrons, released during ionization processes. Here we test the applicability of a classical molecular dynamics scheme in a yet unexplored regime: for a strongly bound molecular system represented by buckminsterfullerene, C60, sin...

Molecular dynamics simulations have been performed on PEO-based polymer nanocomposites and nanocomposite polymer electrolytes. MD simulations revealed that the PEO density is significantly perturbed by TiO2 surfaces, PEO and ion dynamics in the vicinity of nanoparticles was found to be intimately related to the structure of the solid nanoparticle surfaces, polymer-surface interactions and the n...