DNA

DNA is a charged molecule. If we calculate it without explicit water consideration, the repulsion of the charges quickly destroys the helix. Therefore it is necessary to take special arrangements. Options:

• Reduce the charges on the phosphate groups from 1 to 0.3-0.5 electrons
• Use the distance-dependent dielectric constant
• Use Generalized Born model
• Use Sheffield model

Sheffield model is a good compromise between the Generalized Born, which is twice as slow, and the first two methods which are too coarse.