Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems, however, create the need for approximations to the standard MD methods and for uncertainty quantification and reliability assessment of those approximations....

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...

During the past several years, there have been a number of advances in the computational and theoretical modeling of lipid bilayer structural and dynamical properties. Molecular dynamics (MD) simulations have increased in length and time scales by about an order of magnitude. MD simulations continue to be applied to more complex systems, including mixed bilayers and bilayer self-assembly. A cri...

We present a Bayesian probabilistic framework for quantifying and propagating the uncertainties in the parameters of force fields employed in molecular dynamics (MD) simulations. We propose a highly parallel implementation of the transitional Markov chain Monte Carlo for populating the posterior probability distribution of the MD force-field parameters. Efficient scheduling algorithms are propo...

Both atomic force microscopy (AFM) experiments and molecular dynamics (MD) simulation are carried out to investigate atomic stick-slip friction by sliding a Pt tip on an Au substrate. Efforts are taken to match the conditions for AFM experiment and MD simulation as closely as possible. The results show that AFM and MD provide consistent energetic parameters, which suggests that MD simulations c...

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 ...

Classical molecular dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational protocol based on a clustering approach following standard MD simulations. The MD simulations are performed by using a recently published classical interaction ...

Solution state x-ray diffraction fingerprinting is demonstrated as a method for experimentally assessing the accuracy of molecular dynamics (MD) simulations. Fourier transforms of coordinate data from MD simulations are used to produce reciprocal space "fingerprints" of atomic pair distance correlations that are characteristic of the ensemble and are the direct numerical analogues of experiment...

Molecular Dynamics (MD) and Monte Carlo (MC) simulations are the most popular simulation techniques for many-particle systems. Although they are often applied to similar systems, it is unclear to which extent one has to expect quantitative agreement of the two simulation techniques. In this work, we present a quantitative comparison of MD and MC simulations in the microcanonical ensemble. For t...

Virtual laboratory MolDynGrid has been established for computational researches in structural biology and bioinformatics, especially for molecular dynamics (MD) simulations of biological macromolecules and their complexes. Biomolecular simulation usually requires a very high processing power and huge storage space for MD trajectories. In this study we describe the development of virtual laborat...