Molecular dynamics simulations of the d(CCAACGTTGG)2 decamer in crystal environment: Comparison of atomic point-charge, extra-point, and polarizable force fields
- 8 October 2004
- journal article
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 121 (14) , 6998-7008
- https://doi.org/10.1063/1.1788631
Abstract
Molecular dynamics simulations of the DNA duplex d(CCAACGTTGG)(2) were used to study the relationship between DNA sequence and structure in a crystal environment. Three different force fields were used: a traditional description based on atomic point charges, a polarizable force field, and an "extra-point" force field (with additional charges on extranuclear sites). It is found that all the force fields reproduce fairly well the sequence-dependent features of the experimental structure. The polarizable force field, however, provides the most accurate representation of the crystal structure and the sequence-dependent effects observed in the experiment. These results point out to the need of the inclusion of polarization for accurate descriptions of DNA.Keywords
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