Polymorphic transitions in single crystals: A new molecular dynamics method

Abstract

A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in solids under external stress and at finite temperature. As an example of the use of this technique we show how a single crystal of Ni behaves under uniform uniaxial compressive and tensile loads. This work confirms some of the results of static (i.e., zero temperature) calculations reported in the literature. We also show that some results regarding the stress-strain relation obtained by static calculations are invalid at finite temperature. We find that, under compressive loading, our model of Ni shows a bifurcation in its stress-strain relation; this bifurcation provides a link in configuration space between cubic and hexagonal close packing. It is suggested that such a transformation could perhaps be observed experimentally under extreme conditions of shock.

Structure of the full-length glucagon class B G-protein-coupled receptor

“…The temperature of the systems was maintained at 310 K using the v-rescale method 39 with a coupling time of 0.1 ps. The pressure was kept at 1 bar using the Parrinello-Rahman 40 with τ p = 1.0 ps and a compressibility of 4.5 × 10 −5 bar −1 . SETTLE 41 constraints and LINCS 42 constraints were applied to the hydrogen-involved covalent bonds in water molecules and in other molecules, respectively, and the time step was set to 2 fs.…”

Molecular Dynamics Study of the Interface between Water and 2-Nitrophenyl Octyl Ether

“…The Nosé-Hoover thermostat 39,40 was applied to control the temperature at 298 K, while the normal pressure was kept at 1 bar using the semi-isotropic form of the Parrinello-Rahman barostat 41 . The interfacial systems were constructed by first equilibrating two separate boxes containing the water and organic liquids with the same cross-sectional dimensions.…”

Low-temperature and high-pressure induced swelling of a hydrophobic polymer-chain in aqueous solution

“…For completeness, a detailed simulation protocol is given in Table I. The MD-simulations are carried out in the NPT ensemble using the Nosé-Hoover thermostat [51,52] and the Rahman-Parrinello barostat [53,54] with coupling times τ T = 1.5 ps and τ p = 2.5 ps (assuming an isothermal compressibility of χ T = 4.5 10 −5 bar −1 ), respectively. The electrostatic interactions are treated in the "full potential" approach by the smooth particle mesh Ewald summation [55] with a real space cutoff of 0.9 nm and a mesh spacing of approximately 0.12 nm and 4th order interpolation.…”