EFFICIENT STRESS-RELAXATION IN MOLECULAR-DYNAMICS SIMULATIONS OF SEMIFLEXIBLE N-ALKANES

We perform isobaric-isothermal molecular dynamics simulations of parti ally rigid,l-alkanes of length 10 (10 carbon atoms) and 32, respective ly. All bonds an considered as rigid. For these systems we compare mol ecular and atomic scaling to control the pressure in the Nose-Andersen simulation scheme [S. Nose, J. Chem. Phys, 81, 511 (1984); H. C. Ande rsen, ibid. 72, 2384 (1980)]. Atomic scaling in the presence of geomet rical constraints means coupling all available degrees of freedom to t he pressure bath, keeping the desired isobaric-isothermal ensemble, an d satisfying at the same time the geometrical constraints. The corresp onding equations of motion have been derived recently [G. R. Kneller a nd T. Mulders, Phys. Rev. E 54, 6825 (1996)]. In contrast, no intramol ecular degrees of freedom but only the center-of-mass positions are co upled to the pressure bath when the well established molecular scaling is applied. We demonstrate that coupling the intramolecular degrees o f freedom to the volume dynamics (or, equivalently, to the pressure ba th) 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 e xplicitly 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 expe riments. [S1063-651X(98)02511-2].