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New nonbonded interactions calculation strategy for rectangular systems. I. Preliminary molecular dynamics study of solvated Na + ion
Author(s) -
Ledauphin V.,
Vergoten G.
Publication year - 2000
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/1097-0282(2000)57:6<373::aid-bip70>3.0.co;2-p
Subject(s) - chemistry , molecular dynamics , ion , chemical physics , dynamics (music) , computational chemistry , nanotechnology , organic chemistry , physics , materials science , acoustics
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. © 2000 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 57: 325–328, 2000