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.

dna.txt · Last modified: 2014/01/25 04:45 (external edit)
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