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Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
Author(s) -
Prabhu Ninad V.,
Panda Manoranjan,
Yang Qingyi,
Sharp Kim A.
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20874
Subject(s) - molecular dynamics , chemistry , electrostatics , solvation , ion , water model , counterion , solvent models , chemical physics , ewald summation , computational chemistry , ionic bonding , hydrogen bond , implicit solvation , nucleic acid , molecule , organic chemistry , biochemistry
An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter‐ions, co‐ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion electrostatics is treated within the FDP model when close to the solute, and by the Coulombic model when far from the solute. The two zone model reduces computation time, but retains an accurate treatment of the ion atmosphere electrostatics near the solute. Ion compositions can be set to reproduce specific ionic strengths. The entire ion/water treatment is interfaced with the molecular dynamics package CHARMM. Using the CHARMM‐ZAPI software combination, the implicit solvent model was tested on A and B form duplex DNA, and tetraloop RNA, producing stable simulations with structures remaining close to experiment. The model also reproduced the A to B duplex DNA transition. The effect of ionic strength, and the structure of the counterion atmosphere around B form duplex DNA were also examined. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008