[[dna]]
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.
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