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® Applications in Behavior Analysis of Systems Consisting of Carbon Nanotubes through Molecular Dynamics Simulation
Published in Sarhan M. Musa, ®, 2018
Masumeh Foroutan, Sepideh Khoee
Molecular dynamics simulations were performed in Tinker molecular modeling package (version 5.0)136 using the MM3 force field.137 The MM3 force field has been considered to calculate the structures and energies, including heats of formation, conformational energies, and rotational barriers for hydrocarbons more accurately than was possible with earlier force fields.137 The total potential energy (Etotal) of our simulated systems is calculated as the sum of the eight individual energy terms including () Etotal=Es+Eθ+Eω+ESθ+EωS+Eωθ+Eθθ′+Evdw
Significance of molecular-level behaviour incorporation in the constitutive models of expansive clays – a review
Published in Geomechanics and Geoengineering, 2018
The potential function used by Sato et al. (2001) and Ichikawa et al. (2002) in the simulation of several clay minerals was adopted in the study by Ponder (2011) to simulate the minerals. The function consists of combinations of several potentials including Coulomb (attractive or repulsive), Born–Mayer–Higgins short-range repulsion, van der Waals and Morse terms. In this study, TINKER software (Ponder 2011) was used for the MD simulations. Data input included the initial configuration of the atomic structures and the interatomic potentials chosen appropriately for the particular mineral. For all the simulations, an NPT (constant number of particles N, pressure P and temperature T) ensemble was used to obtain the stress–strain response of the minerals. The results of the simulations, as shown, reveal a general agreement between the measured and known values of moduli for the minerals except for Kaolinite. The authors have attributed the anomalously higher modulus value of Kaolinite to the molecular arrangement at the crystal lattice level.
Continuous version of a square-well potential of variable range and its application in molecular dynamics simulations
Published in Molecular Physics, 2018
I. M. Zerón, C. Vega, A. L. Benavides
Simulation studies for discrete potentials have been mostly performed with Monte Carlo (MC) techniques [33–54]. Due to their discontinuities, these kinds of potentials have not been treated by conventional molecular dynamics (MD) simulation that is a very important technique that has been applied to many continuous potentials and successfully incorporated in more general popular simulation packages (GROMACS [55–61], CHARMM [62], DL_POLY [63], EXPResSo [64], IMD [65], LAMMPS [66], ls1 mardyn [67], NAMD [68], TINKER [69], HOOMD [70,71], etc.) to study a great variety of complex systems. Besides, MD simulation has the advantage over the MC method that one can obtain the transport properties of a given potential.