Literature DB >> 20815558

Molecular dynamics simulation with weak coupling to heat and material baths.

Hossein Eslami1, Fatemeh Mojahedi, Jalil Moghadasi.   

Abstract

A method for performing molecular dynamics simulation in the grand canonical ensemble is developed. The molecular dynamics, with coupling to an external bath, simulation method of [Berendsen et al., J. Chem. Phys. 81, 3684 (1984)] is extended for this purpose. Here the physical system of interest consists of real indistinguishable particles plus one fractional particle, whose potential energy of interaction with the rest of particles is scaled by a coupling parameter, ranging dynamically between zero and one. This coupling changes the number of particles in the system gradually and dynamically, depending on the target values of the excess chemical potential, temperature, and volume. A nonlinear scaling scheme has been adopted to scale the potential energy of interaction of the fractional particle with the rest of the system. The method has been employed to predict the density of compressed Lennard-Jones fluid, compatible with the target values of temperature and the excess chemical potential, over a wide range of temperatures and densities. The method has further been applied to do molecular dynamics simulation in the grand canonical ensemble for water and to predict its vapor-liquid phase coexistence point. The results obtained using this method are in complete agreement with previously reported results in the literature.

Entities:  

Year:  2010        PMID: 20815558     DOI: 10.1063/1.3474951

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  12 in total

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10.  Effective Drug Concentration and Selectivity Depends on Fraction of Primitive Cells.

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