New nonbonded interactions calculation strategy for rectangular systems. I. Preliminary molecular dynamics study of solvated Na(+) ion.
A new molecular nonbonded interactions treatment strategy is proposed in the context of rectangular periodic boundary conditions simulations. Several molecular dynamics simulations are performed on a sodium ion in aqueous solution. Box sizes are modified from a cubic to a rectangular shape. The results are compared with those found using a classical spherical cutoff. This new method yields ion-oxygen radial distribution functions in good agreement with experimental results, thus showing its reliability. Severe perturbations in the structural orientation of water molecules in the first shell with the increase of the box length are observed under the classical cutoff method. However, these distorting effects are reduced with the present nonbonded interactions treatment.
Ledauphin
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CRESIMM, Université des Sciences et Technologies de Lille, UFR de Chimie, Bâtement C8, 59655 Villeneuve d'Ascq Cedex, France.
Vergoten
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D000465:Algorithms; D002414:Cations, Monovalent / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry; D008958:Models, Molecular; D012964:Sodium / Q000737:chemistry*; D012997:Solvents; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D002414:Cations, Monovalent; D008051:Lipid Bilayers; D012997:Solvents; D014867:Water; D012964:Sodium