Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 28, Issue 6, Pages 1091-1099Publisher
WILEY
DOI: 10.1002/jcc.20557
Keywords
pi-pi interaction; molecular dynamics simulation; Morse-type potential function; protein structure; drug-binding conformation
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No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation. (C) 2007 Wiley Periodicals, Inc.
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