Paper Citing NAMD - Abstract
Jover, J.; Haslam, A. J.; Galindo, A.; Jackson, G.; Mueller, E. A.
Pseudo hard-sphere potential for use in continuous molecular-dynamics simulation of spherical and chain molecules
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 144505, OCT 14 2012
We present a continuous pseudo-hard-sphere potential based on a cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). Using this potential one can mimic the volumetric, structural, and dynamic properties of the discontinuous hard-sphere potential over the whole fluid range. The continuous pseudo potential has the advantage that it may be incorporated directly into off-the-shelf molecular-dynamics code, allowing the user to capitalise on existing hardware and software advances. Simulation results for the compressibility factor of the fluid and solid phases of our pseudo hard spheres are presented and compared both to the Carnahan-Starling equation of state of the fluid and published data, the differences being indistinguishable within simulation uncertainty. The specific form of the potential is employed to simulate flexible chains formed from these pseudo hard spheres at contact (pearl-necklace model) for m(c) = 4, 5, 7, 8, 16, 20, 100, 201, and 500 monomer segments. The compressibility factor of the chains per unit of monomer, mc, approaches a limiting value at reasonably small values, m(c) < 50, as predicted by Wertheim's first order thermodynamic perturbation theory. Simulation results are also presented for highly asymmetric mixtures of pseudo hard spheres, with diameter ratios of 3: 1, 5: 1, 20: 1 over the whole composition range. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4754275]
