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DYNGA: a general purpose QM-MM-MD program. I. Application to water

  1. Author:
    Parker, C. L.
    Ventura, O. N.
    Burt, S. K.
    Cachau, R. E.

  2. Author Address

    NCI, Adv Biomed Comp Ctr, SAIC, Frederick, MD 21702 USA NCI, Adv Biomed Comp Ctr, SAIC, Frederick, MD 21702 USA UDELAR, Fac Quim, DEQUIFIM, CCPG, Montevideo 11800, Uruguay Cachau RE NCI, Adv Biomed Comp Ctr, SAIC, Frederick, MD 21702 USA
    1. Year: 2003
  2. Journal: Molecular Physics
    1. 101
    2. 17
    3. Pages: 2659-2668
  4. Type of Article: Article
  1. Abstract:

    We present a general purpose QM-MM-MD engine (DYNGA) designed to test alternative hybrid Hamiltonians geared towards the treatment of problems of interest in structural biology including the use of experimental data constraints. In this first presentation we use DYNGA to explore the behaviour of a traditional QM-MM approach in the treatment of the water-water interaction. We find the potential energy hypersurface for the water dimer computed with the HF 4-31G*/TIP3P hybrid Hamiltonian tends to be too. at. We also explore the effect of using traditional QM-MM techniques on proton wires and conclude there is a need for improvement, possibly addressed by using polarizable force fields.

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