Journal of the American Chemical Society, Vol.119, No.25, 5934-5938, 1997
Molecular-Dynamics Simulations of DNA with Proteins Consistent Gromos Force-Field and the Role of Counterions Symmetry
Model solvent effects, related to DNA stability in water, are explored with molecular dynamics (MD) simulations : (i) hydrophobicity and (ii) salt modulated electrostatic effects. The 2.6 Angstrom resolution X-ray coordinates of the DNA oligomer from Zif268 are used to seed the MD simulations. The molecular model contains fully charged and geometrically unrestricted 10 base-pairs DNA in a 2640 water molecules bath with 18 Na-ions at 298 K. (i) The hydrophobicity correction affects the water-oxygen repulsive (root C12(Ow,Ow)) parameter that transforms the "hydrophilic" united carbon atom in the old GROMOS-87 force field into an hydrophobic one. The root mean square (rms) deviations stay below 2.8 Angstrom, and the 600 ps-averaged and regularized structure elicits the positive effect of this correction on the structure. (ii) The electrostatic effects are probed by constructing a distribution of counterions placed in between phosphate groups at the end of a collective equilibration; salt (co-ion) effects are modeled by imposing a weak harmonic constraint (0.58 kcal mol(-1) Angstrom(-2)) to the equilibrated set of counterions. A 1 ns trajectory shows rms deviations from X-ray below 1.7 Angstrom for all atoms at 600 ps and below 2.3 Angstrom in the time span up to 1 ns; counterions fluctuations are large enough to allow for DNA bending and conformational changes. The quality of this simulation can be appreciated from different averaged and regularized structures. The structural results are comparable to those obtained with state-of-the-art force fields using Ewald summation technique for an oligonucleotide of similar size.