A coarse-grained model of DNA with explicit solvation by water and ions.

ABSTRACT: Solvation by water and ions has been shown to be vitally important for biological molecules, yet fully atomistic simulations of large biomolecules remain a challenge due to their high computational cost. The effect of solvation is the most pronounced in polyelectrolytes, of which DNA is a paradigmatic example. Coarse-grained (CG) representations have been developed to model the essential physics of the DNA molecule, yet almost without exception, these models replace the water and ions by implicit solvation in order to significantly reduce the computational expense. This work introduces the first coarse-grained model of DNA solvated explicitly with water and ions. To this end, we combined two established CG models; the recently developed mW-ion model [DeMille, R. C.; Molinero, V. J. Chem. P

SUBMITTER: DeMille RC 

PROVIDER: S-EPMC3019136 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature