Efficient stress relaxation in molecular dynamics simulations of semiflexible n -alkanes

International audienceWe perform isobaric-isothermal molecular dynamics simulations of partially rigid n-alkanes of length 10 (10 carbon atoms) and 32, respectively. All bonds are considered as rigid. For these systems we compare molecular and atomic scaling to control the pressure in the Nosé-Andersen simulation scheme [S. Nosé, J. Chem. Phys. 81, 511 (1984); H. C. Andersen, ibid. 72, 2384 (1980)]. Atomic scaling in the presence of geometrical constraints means coupling all available degrees of freedom to the pressure bath, keeping the desired isobaric-isothermal ensemble, and satisfying at the same time the geometrical constraints. The corresponding equations of motion have been derived recently [G. R. Kneller and T. Mülders, Phys. Rev. E 54, 6825 (1996)]. In contrast, no intramolecular degrees of freedom but only the center-of-mass positions are coupled to the pressure bath when the well established molecular scaling is applied. We demonstrate that coupling the intramolecular degrees of freedom to the volume dynamics (or, equivalently, to the pressure bath) strongly improves the relaxation of energy and volume for the long chains, while for the short chains atomic and molecular scalings are more or less equivalent in this respect. For the long chains we show explicitly that the barostat couples to intramolecular breathing modes when atomic scaling is used. The frequencies of these modes are found to be in excellent agreement with results from neutron scattering experiments