MOLECULAR DYNAMICS SIMULATIONS & METHOD DEVELOPMENT

利用计算机图形学实验室的设施展示 并对分子动力学模拟结果进行分析。我们的研究 项目的重点是a)进一步完善和测试新一代 要使用的附加和非附加力场参数的 分子力学和动力学计算，以及b)大分子 使用分子动力学进行模拟。新的琥珀力场是 在分子动力学模拟中得到了广泛的检验 分子，特别关注DNA模拟。无拘无束 分子动力学模拟已被应用于模拟 脱氧核糖十二聚体双链d(CGCGAATTCGCG)2及其磷酰胺 (N-P)类似物在水溶液中。计算发现，3‘ 磷酰胺修饰的DNA双链经历B到A的转变 而正常的DNA是A到B的转变，这证实了实验 观察并证明新的琥珀力场的质量 参数化。将新的琥珀参数化法应用于研究 小分子的构象平衡。琥珀 参数化正在扩展，以包括非相加效果和 孤立对相互作用。

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.