====== DNA ======

{{ :dickerson_cgcgaattcgcg.png?200|Dickerson dodecanucleotide CGCGAATTCGCG}}

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.