Molecular Dynamics Simulations of Biomolecules in Water

  • K. N. Swamy
  • Enrico Clementi


Following our previous studies on understanding the structure and dynamics of biomolecules in water we have performed molecular dynamics (MD) simulations for the following systems: i) the ion transport through Gramicidin A (GA) transmembrane channel, and ii) the hydration structure and dynamics of B and Z-DNA in the presence of counterions (K+). The results of these simulations are presented both for the structural and dynamical properties. In the case of gramicidin the results are most preliminary and seem to indicate that the waters close to the ion inside the channel point their dipoles towards the ion, while the waters away from the ion are influenced by the bulk waters. In the simulations of B and Z-DNA we find that the waters close to the helix retain their memory of their initial orientations for longer times than those waters away from the helix, in agreement with the relaxation studies of Lindsay et al. on Z-DNA. Further, the velocity auto correlation functions for the counterions (K+) exhibit a caged behavior unlike that in an ionic solution.


Water Molecule Molecular Dynamic Simulation Monte Carlo Radial Distribution Function Bulk Water 
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Copyright information

© Plenum Press, New York 1986

Authors and Affiliations

  • K. N. Swamy
    • 1
    • 2
  • Enrico Clementi
    • 1
    • 2
  1. 1.Data Systems Division, Dept. 48B MS 428IBM CorporationKingstonUSA
  2. 2.National Foundation for Cancer ResearchBethesdaUSA

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