Large-scale atomic/molecular

The GBEMP model requires some additional infrastructure beyond that found in standard molecular dynamics codes. For example, because the CG particles are elliptical, they have a net orientation that must be tracked and integrated during the simulation this is most easily done using a rigid-body integrator. For this reason, we chose LAMMPS (Large-scale Atomic/Molecular... 

Large-scale atomic/ molecular massively parallel simulator (LAMMPS) code 0.788 for armchair 1.176 for zigzag Effects of chirality and Van der Waals interaction on Young s modulus, elastic compressive modulus, bending, tensile, compressive stiffness, and critical axial force of DWCNTs... 

LAMMPS—Large-scale Atomic/Molecular Massively Parallel Simulator, Sandia National... 

An important characteristic of biomolecular motion is that the different types of motion are interdependent and coupled to one another. For example, a large-scale dynamic transition cannot occur without involving several medium-scale motions, such as helix rearrangements. Medium-scale motions cannot occur without involving small-scale motions, such as side-chain movement. Finally, even side-chain motions cannot occur without the presence of the very fast atomic fluctuations, which can be viewed as the lubricant that enables the whole molecular construction to move. From the point of view of dynamic... 

It has been observed that cobalt may undergo large-scale reconstruction under a synthesis gas environment.27 Reconstruction is a thermodynamically driven process that results in the stabilization of less reactive surfaces. Recent molecular modeling calculations have shown that atomic carbon can induce the clock reconstruction of an fee cobalt (100) surface.28 It has also been postulated and shown with in situ x-ray adsorption spectroscopy (XAS) on cobalt supported on carbon nanofibers that small particles (<6 nm) undergo a reconstruction during FTS that can result in decreased activity.29... 

Principal component analysis (PCA) is another tool that has been used extensively to analyze molecular simulations. The technique, which attempts to extract the large-scale characteristic motions from a structural ensemble, was first applied to biomolecular simulations by Garcia [28], although an analogous technique was used by Levy et al. [30]. The first step is the construction of the 3N x 3N (for an N-atom system) fluctuation correlation matrix... 

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