MOLECULAR DYNAMICS SIMULATIONS & METHOD DEVELOPMENT

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The Computer Graphics Laboratory facilities were used to display and analyze molecular dynamics simulations results. Our research projects focus on a) further refining and testing the new generation of additive and nona dditive force field parameters to be used in molecular mechanics and dynamics calculations, and b) macromolecular simulation using molecular dynamics. The new AMBER force field was extensively tested in molecular dynamics simulations for large molecules, with special focus on DNA simulation. Unrestrained molecular dynamics simulations have been applied to simulate deoxyribose dodecamer duplex d(CGCGAATTCGCG)2 and its phosphoramidate (N-P) analog in water solution. The calculations find that 3' phosphoramidate modified DNA duplexes undergo a B to A transition whereas normal DNA an A to B transition, which confirms experimental observation and proves the quality of the new AMBER force field parametrization. New AMBER parametrization has been applied to study conformational equilibria of small molecules. The AMBER parametrization is being extended to include nonadditive effects and lone pairs interactions.