The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with n...

Crystal structure prediction and molecular dynamics methods were applied to the cyclotrimethylene trinitramine (RDX) crystal to explore the stability rankings of various polymorphs using a recently developed nonempirical potential energy function that describes the RDX dimer interactions. The energies of 500 high-density structures resulting from molecular packing were minimized and the 14 lowe...

We demonstrate the stochastic nature of cavitation in a binary metallic liquid Cu46Zr54 during hydrostatic expansion by employing molecular dynamics (MD) simulations using a quantum mechanics (QM)-derived potential. The activation volume is obtained from MD simulations and transition-state theory. Extrapolation of the pressure dependence of the activation volume from our MD simulations to low t...

Full-quantum mechanical fragment molecular orbital-based molecular dynamics (FMO-MD) simulations were applied to the hydration reaction of formaldehyde in water solution under neutral conditions. Two mechanisms, a concerted and a stepwise one, were considered with respect to the nucleophilic addition and the proton transfer. Preliminary molecular orbital calculations by means of polarized conti...

A novel methodology is presented for evaluating a dynamic ensemble of oligosaccharide conformations by lanthanide-assisted NMR spectroscopy combined with molecular dynamics (MD) simulations. The results obtained using the GM3 trisaccharide demonstrated that pseudocontact shift measurements offer a valuable experimental tool for the validation of MD simulations of highly flexible biomolecules.

Communications Correlated motions can be accurately extracted from molecular dynamics (MD) simulations that are compatible with the measured NMR spectroscopic data (NOE and order parameters) for two different proteins (Cov: covariance matrix). B. de Groot and co-workers discuss the results of MD simulations on a fragment of protein G in their Communication on the following pages.

We apply the theoretical formalism developed by us earlier @M. Vergeles and G. Szamel, J. Chem. Phys. 110, 6827 ~1999!# to study density, temperature, and bond-length dependence of the dynamic friction on a molecular bond. We show that the theory reproduces all the trends seen in molecular dynamics ~MD! simulations. The theoretical predictions agree reasonably well with the results of MD simula...

While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD) simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. T...

This paper describes BioPAUÁ project first release of a portal for Molecular Dynamics (MD) using a computational grid environment. It unites MD simulations and analyses tools with grid technologies to provide support to biomolecular structures in silico experiments. BioPAUÁ Project goal is to offer a tool, as well the facility, for researches working in several important fields (e.g., bioinform...

This paper presents a molecular mechanics study of nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics simulation the behavior of bionanorobotic components and structures through 3-D visualization. The main novelty of the proposed simulations is based on the mechanical ch...